LA JOLLA PHARMACEUTICAL CO
S-3/A, 2000-09-01
BIOLOGICAL PRODUCTS, (NO DIAGNOSTIC SUBSTANCES)
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<PAGE>   1


   AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON SEPTEMBER 1, 2000

                                                      REGISTRATION NO. 333-43066

================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                ----------------

                                 PRE-EFFECTIVE
                                AMENDMENT NO. 1

                                       TO

                                    FORM S-3

                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                         LA JOLLA PHARMACEUTICAL COMPANY
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)


           DELAWARE                                             33-0361285
(STATE OR OTHER JURISDICTION OF                               (I.R.S. EMPLOYER
 INCORPORATION OR ORGANIZATION)                              IDENTIFICATION NO.)



                             6455 NANCY RIDGE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (858) 452-6600
              (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER,
       INCLUDING AREA CODE, OF REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)




                                 STEVEN B. ENGLE
                         LA JOLLA PHARMACEUTICAL COMPANY
                             6455 NANCY RIDGE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (858) 452-6600
            (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER,
                   INCLUDING AREA CODE, OF AGENT FOR SERVICE)




                                    COPY TO:
                             LEONARD J. MCGILL, ESQ.
                           GIBSON, DUNN & CRUTCHER LLP
                                  4 PARK PLAZA
                            IRVINE, CALIFORNIA 92614
                                 (949) 451-3800



          APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO PUBLIC:
     From time to time after this registration statement becomes effective.

         If any of the securities being registered on this form are to be
offered pursuant to dividend or interest reinvestment plans, please check the
following box. [ ]

         If any of the securities being registered on this Form are to be
offered on a delayed or continuous basis pursuant to Rule 415 under the
Securities Act of 1933, other than securities offered only in connection with
dividend or interest reinvestment plans, check the following box. [X]

         If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering. [ ]

         If this Form is a post-effective amendment filed pursuant to Rule
462(c) under the Securities Act, check the following box and list the Securities
Act registration statement number of the earlier effective registration
statement for the same offering. [ ]

         If delivery of the prospectus is expected to be made pursuant to Rule
434, please check the following box. [ ]

                            -------------------------

                         CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>
===============================================================================================================================
                                           AMOUNT             PROPOSED MAXIMUM          PROPOSED MAXIMUM
        TITLE OF SECURITIES                 TO BE            OFFERING PRICE PER        AGGREGATE OFFERING         AMOUNT OF
          TO BE REGISTERED              REGISTERED(1)             SHARE(2)                  PRICE(2)           REGISTRATION FEE
-------------------------------------------------------------------------------------------------------------------------------
<S>                                     <C>                  <C>                       <C>                     <C>
           Common Stock,                  4,800,000                $6.66                   31,968,000               $8,440
     par value $0.01 per share
===============================================================================================================================
</TABLE>

(1)  Each share of Common Stock includes a right to purchase one one-thousandth
     of a share of Series A Junior Participating Preferred Stock pursuant to the
     Rights Agreement between the Registrant and American Stock Transfer & Trust
     Company, as Rights Agent.

(2)  Estimated solely for the purpose of calculating the registration fee
     pursuant to Rules 457(c) and 457(h) and based on the average of the high
     and the low price of the Common Stock of the Registrant as reported on
     August 1, 2000 on the Nasdaq National Market System.

THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR DATES
AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL FILE
A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION STATEMENT
SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF THE
SECURITIES ACT OF 1933, AS AMENDED, OR UNTIL THE REGISTRATION STATEMENT SHALL
BECOME EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID
SECTION 8(a), MAY DETERMINE.

================================================================================

<PAGE>   2

PROSPECTUS

                                   [LJP LOGO]



                                4,800,000 Shares
                                  Common Stock

         This prospectus relates to 4,800,000 shares of our common stock that
may be sold from time to time by the selling stockholders named in this
prospectus. The selling stockholders acquired these shares of our common stock
in private transactions.

         This offering is not being underwritten. The selling stockholders may
offer the shares through public or private transactions at the market price for
our common stock at the time of the sale, a price related to the market price, a
negotiated price or such other prices as the selling stockholders determine from
time to time. See "Plan of Distribution" on page 11.

         All of the net proceeds from the sale of these shares of common stock
will go to the selling stockholders. We will not receive any proceeds from sales
of these shares.

         Our common stock is traded on the Nasdaq National Market under the
symbol "LJPC." On August 30, 2000, the last reported sale price of our common
stock was $6.625 per share.


         You should read this prospectus carefully before you invest.


         Investing in our common stock involves substantial risks. See "Risk
Factors" beginning on page 2.


                                ----------------


         Neither the Securities and Exchange Commission nor any state securities
commission has approved or disapproved these securities or determined if this
prospectus is truthful or complete. Any representation to the contrary is a
criminal offense.

         The information in this prospectus is not complete and may be changed.
These securities will not be sold until the registration statement filed with
the Securities and Exchange Commission is effective. This prospectus is not an
offer to sell these securities and it is not soliciting an offer to buy these
securities in any state where the offer or sale is not permitted.

                                ----------------


                The date of this prospectus is September 1, 2000


<PAGE>   3

                         LA JOLLA PHARMACEUTICAL COMPANY


         La Jolla Pharmaceutical Company is a biopharmaceutical company focused
on the research and development of therapeutic products for the treatment of
some life-threatening antibody-mediated diseases. Antibody-mediated diseases are
the result of a malfunction of the body's immune system, in which cells in the
immune system produce disease-causing antibodies. These diseases include
autoimmune conditions such as lupus and antibody-mediated stroke. Current
treatments for these autoimmune disorders target the symptoms of the disease or
generally suppress the normal operation of the immune system, frequently
resulting in severe negative side effects and hospitalization. Our drug
candidates are designed to treat the underlying cause of many antibody-mediated
diseases without these side effects. Our clinical drug candidate is known as LJP
394, a lupus treatment drug.

         We are registering for resale a total of up to 4,800,000 shares of our
common stock previously sold by us to investors in private transactions. These
investors are identified in the section headed "Selling Stockholders." We will
not receive any of the proceeds for the resale of these shares.


         We are incorporated in the State of Delaware. Our principal executive
offices are located at 6455 Nancy Ridge Drive, San Diego, California 92121 and
our telephone number is (858) 452-6600.




                                  RISK FACTORS


         An investment in our common stock involves a high degree of risk. You
should carefully consider the following risk factors related to our common stock
offered by this prospectus and to our business and operations. You should also
carefully consider the other information in this prospectus and in the documents
incorporated by reference. Some of these factors have affected our financial
condition and operating results in the past or are currently affecting us. All
of these factors could affect our future financial condition or operating
results. If any of the following risks actually occurs, our business could be
harmed. If that happens, the trading price of our common stock could decline,
and you may lose all or part of your investment.






                                       2
<PAGE>   4


I. RISK FACTORS RELATING TO LA JOLLA PHARMACEUTICAL AND THE INDUSTRY IN
   WHICH WE OPERATE.

Our drug candidates may not perform well in clinical trials and we may not be
permitted to conduct further clinical trials. Without successful clinical
trials, we will not be able to market or sell any products.

         If LJP 394 is ultimately not found to be safe and effective, we would
be unable to obtain regulatory approval for its commercialization. Because LJP
394 is our only drug candidate that has advanced to clinical trials, and because
there is no guarantee that we would be able to develop an alternate drug
candidate, our inability to commercialize LJP 394 would have a severe negative
effect on our business, including revenues and profits.

         In order to sell our products that are under development, we must first
receive regulatory approval. To obtain regulatory approval, we must conduct
clinical studies demonstrating that our products are safe and effective.
Although LJP 394 appears promising, it may not be successful in future clinical
trials. Our prior clinical study of LJP 394, in collaboration with Abbott, was
halted, and the forthcoming Phase III clinical study may also be delayed or
halted for various reasons, including:

         o  the product is not effective, or physicians think that it is not
            effective,

         o  patients experience severe side effects during treatment,

         o  patients do not enroll in the study at the rate we expect, or

         o  product supplies are not sufficient to treat the patients in the
            study.

         In addition, the FDA and foreign regulatory authorities have
substantial discretion in the approval process. The FDA and foreign regulatory
authorities may not agree that we have demonstrated that LJP 394 is safe and
effective after we complete clinical trials. Even if the results of prior
clinical trials are positive, the FDA may require us to design and conduct
additional studies, which may result in significant expense and delay. The FDA
may require new clinical trials because of inconclusive results from earlier
clinical trials, a possible failure to conduct prior clinical trials in complete
adherence to FDA good clinical practice standards and identification of new
clinical trial endpoints.

Our products are in the early stage of development and the technology underlying
our products is uncertain and unproven. If our products cannot be successfully
developed, we will never be able to generate meaningful sales.

         All of our product development efforts are based on unproven
technologies and therapeutic approaches that have not been widely tested or
used. LJP 394 has not been proven to be effective in humans and the technology
on which it is based has been used only in our preclinical tests and clinical
trials. If our products or technology is not effective, we will not generate
meaningful sales. Application of LJP 394's technology to antibody-mediated
diseases other than lupus is in even earlier research stages.

         LJP 394 and our other potential drug candidates require significant
additional research and development and are subject to significant risks.
Potential products that appear to be promising at early stages of development
may nevertheless fail to reach market or become profitable for some of the
following reasons:


         o  products may be ineffective or cause harmful side effects during
            preclinical testing or clinical trials,

         o  products may fail to receive necessary regulatory approvals,

         o  products may be difficult to manufacture,

         o  products may be uneconomical to produce particularly if high dosages
            are required,


         o  products may fail to achieve market acceptance,

         o  products may be precluded from commercialization because of
            proprietary rights of third parties, and


         o  competitors may develop superior products.


                                       3
<PAGE>   5


         The technology underlying LJP 394 appears effective in humans. However,
no products have been developed to date that use our technology. There is no
guarantee that LJP 394 will work as intended. Furthermore, clinical trials of
LJP 394 may be viewed as a test of LJP's entire approach to developing therapies
for antibody-mediated diseases. If the data from our clinical trials indicates
that LJP 394 is ineffective, the applicability of our technology to other
antibody-mediated diseases will be highly uncertain. Therefore, there is
significant risk that our therapeutic approaches will not prove to be
successful, and there can be no guarantee that our drug discovery technologies
will result in any commercially successful products.


Our success in developing our products and marketing them successfully depends
significantly upon our ability to obtain patent protection for LJP 394 and any
other developed products. In addition, we will need to successfully preserve our
trade secrets and operate without infringing on the rights of others.


         We will depend on patents and other unpatented intellectual property to
prevent others from profiting from products or technologies that we may have
developed, and to preserve our freedom to operate our business. We own 86 issued
patents and 59 pending patent applications covering various technologies and
drug candidates. However, there can be no assurance that any additional patents
will be issued, or that the scope of any patent protection will be sufficient,
or that any current or future issued patent will be held valid if subsequently
challenged. There is a substantial backlog of biotechnology patent applications
at the U.S. Patent and Trademark Office that may delay the review and issuance
of any patents. The patent position of biotechnology firms like ours generally
is highly uncertain and involves complex legal and factual questions, and no
consistent policy has emerged regarding the breadth of claims covered in
biotechnology patents or protection afforded by these patents. Presently, we
have a number of patent applications pending in the United States relating to
our technology, as well as foreign counterparts to some of our U.S. patent
applications. We intend to continue to file applications as appropriate for
patents covering both our products and processes. There can be no assurance that
patents will be issued from any of these applications, or that the scope of any
issued patents will protect our technology.


         We are aware of one U.S. patent grant that contains claims covering
subject matter that may conflict with some of our key patents and patent
applications, and that may affect our ability to develop and sell our products.
Any conflict between our patents and patent applications, and patents or patent
applications of third parties, could result in a significant reduction of the
coverage of our existing patents or any future patents that may be issued. This
could have a negative effect on our ability to prevent competitors from
profiting from our products and technologies, and this could affect our future
sales. In addition, we may have to incur significant expenses in defending our
patents.


         If the U.S. Patent and Trademark Office or any foreign counterpart
issues or has issued to a competitor patents containing competitive or
conflicting claims, and if these claims are valid, there can be no guarantee
that we would be able to obtain licenses to these patents, that any licensing
fees would be reasonable, or that we would be able to develop or obtain
alternative technology. Patent applications in the United States are kept secret
until a patent is issued. As a result, we do not know if others, including
competitors, have filed patent applications for technology covered by our
pending applications, nor can we be certain that we were the first to invent or
to file patent applications for our technologies. Competitors may have patents
or patent applications pending that relate to compounds or processes that
overlap or compete with our intellectual property.

         We also rely on unpatented intellectual property such as trade secrets
and improvements, know-how, and continuing technological innovation. While we
seek to protect these rights, it is possible that:

         o  inventions relevant to our business will be developed by a person
            not bound by an LJP invention assignment agreement,

         o  binding LJP confidentiality agreements will be breached and we will
            not have adequate remedies for such a breach, or

         o  our trade secrets will otherwise become known or be independently
            discovered by competitors.

         We could incur substantial costs in defending suits brought against us
by others for infringement of intellectual property rights or in prosecuting
suits that we might bring against others to protect our intellectual property
rights.


                                       4
<PAGE>   6

We have a history of losses and may not become profitable.


         We have incurred operating losses each year since our inception in 1989
and had an accumulated deficit of approximately $77.6 million as of June 30,
2000. Our losses are likely to exceed those experienced in prior years due to
the termination of a collaborative relationship with Abbott, unless we are
successful in establishing additional collaborative relationships to help
finance our research and development costs. To achieve profitability we must,
among other things, complete the development of our products, obtain all
necessary regulatory approvals and establish commercial manufacturing and
marketing capabilities. We expect to incur significant losses each year for at
least the next several years as our clinical trial, research, development and
manufacturing scale-up activities increase. The amount of losses and the time
required by us to reach sustained profitability are highly uncertain, and we do
not expect to generate revenues from the sale of products, if any, for at least
several years. We may never achieve product revenues or profitability.


We will need additional funds to support operations and may need to reduce
operations, sell stock or assets, or merge with another entity to continue
operations.


         Our operations to date have consumed substantial capital resources, and
we will continue to expend substantial and increasing amounts of capital for
research, product development, preclinical testing and clinical trials of drug
candidates, to establish commercial-scale manufacturing capabilities, and to
market potential products. We will need to raise additional funds in some way,
and if we are not able to do so we will not be able to fund our operations.


         Our future capital requirements will depend on many factors, including:

         o  continued scientific progress in our research and development
            programs and the size and complexity of these programs,

         o  the scope and results of preclinical testing and clinical trials,

         o  the time and costs involved in applying for regulatory approvals,

         o  the costs involved in preparing, filing, prosecuting, maintaining
            and enforcing patent claims,

         o  competing technological and market developments,

         o  our ability to establish and maintain collaborative research and
            development arrangements, and

         o  the cost of manufacturing scale-up and effective commercialization
            activities and arrangements.


         We expect to incur substantial and increasing losses each year for at
least the next several years as our clinical trial, research, development and
manufacturing scale-up activities increase. We expect our existing capital
resources (including the capital raised through the sale of stock that may be
offered for resale under this prospectus) will be sufficient to fund our
activities, as currently planned, for approximately the next 24 months. However,
the amounts expended by us for various purposes may vary significantly,
and it is possible that our cash requirements will exceed current projections
and that we will therefore need additional financing sooner than currently
expected. In the future, it is possible that we will not have adequate resources
to support our business activities.

         We actively seek additional funding, including through collaborative
arrangements and public and private financings. Our choice of financing
alternatives may vary from time to time depending upon various factors,
including the market price of our securities, conditions in the financial
markets, and the interest of other entities in strategic transactions with LJP.
There can be no guarantee that additional financing will be available on
acceptable terms, if at all, whether through collaborative arrangement, issuance
of securities, or otherwise. If adequate funds are not available, we may be
required to delay, scale back or eliminate one or more of our research and
development programs or obtain funds through arrangements with collaborative
partners or others that require us to relinquish rights to certain technologies
or potential products. This could have a negative impact on our ability to
develop products, or to achieve profitability if our products are brought to
market. If we do obtain additional funding through sales of securities, your
investment in LJP will be diluted.


                                       5

<PAGE>   7


We may not earn as much income as we hope due to possible changes in healthcare
reimbursement policies.

         The continuing efforts of government and healthcare insurance companies
to reduce the costs of healthcare may reduce the amount of income we can
generate from our products. For example, in certain foreign markets, pricing and
profitability of prescription drugs are subject to government control. In the
United States, we expect that there will continue to be a number of federal and
state proposals to implement similar government controls. In addition,
increasing emphasis on managed care in the United States will continue to put
pressure on drug manufacturers to keep prices down. Cost control initiatives
could reduce the revenue that we receive for any products we may develop and
sell in the future. These cost control measures may also affect the
profitability of companies with whom we may transact business, such as
manufacturers of our products, and thus may have a negative effect on our
ability to continue to work with these companies.

If reimbursement policies of Medicare and healthcare companies are changed so
that it is more difficult for patients to be reimbursed for using our products,
our sales would be reduced and this would reduce our earnings.

         Sales of our products to the patients who will use them will depend on
the patients being reimbursed for the costs of our products. Newly approved
drugs may not be accepted for reimbursement by health insurers or Medicare. It
is possible that these organizations will not offer coverage for our products.
Government and other third-party payors increasingly attempt to contain
healthcare costs by limiting both coverage and the level of reimbursement for
new products. If adequate coverage and reimbursement levels are not provided by
government and other third-party payors for our products, sales of these
products would be negatively affected, and this would have a negative effect on
our earnings.

A number of companies compete with us and we face rapid changes in technology.

         The biotechnology and pharmaceutical industries are subject to rapid
changes in technology. Competition from domestic and foreign biotechnology
companies, large pharmaceutical companies and other institutions is intense and
is expected to increase. A number of companies and institutions are pursuing the
development of pharmaceuticals in our targeted areas, many of which are very
large, and have financial technical, sales and distribution and other resources
substantially greater than ours. The greater resources of these competitors
could enable them to develop competing products more quickly than we are able
to, and to market any competing product more quickly so as to make it extremely
difficult for us to develop a share of the market for these products. These
competitors also include companies that are conducting clinical trials and
preclinical studies for the treatment of lupus. Our competitors may develop or
obtain regulatory approval for products more rapidly than we do. Our competitors
may also develop and market technologies and products that are more effective
than those being developed by us or that would render our technology and
proposed products obsolete or noncompetitive.

We may need to establish collaborative agreements, and this could have a
negative effect on our freedom to operate our business, or profit fully from
sales of our products.

         We may seek to collaborate with pharmaceutical companies to gain access
to their research, drug development, manufacturing, marketing and financial
resources. However, we may not be able to negotiate arrangements with any
collaborative partners on acceptable terms, if at all. Any collaborative
relationships that we enter into may include restrictions on our freedom to
operate our business or to profit fully from the sales of our products.

         Once a collaborative arrangement is established, the collaborative
partner may not continue funding any particular program or may pursue
alternative technologies or develop alternative drug candidates, either alone or
with others, to develop treatments for the diseases we are targeting. Competing
products, developed by a collaborative partner or to which a collaborative
partner has rights, may result in the collaborative partner withdrawing support
as to all or a portion of our technology.

         Without collaborative arrangements, we must fund our own research and
development activities, accelerating the depletion of our capital and requiring
us to develop our own marketing capabilities. Therefore, if we are unable to
establish and maintain collaborative arrangements, we could experience a
material adverse effect on our ability to develop products and, once developed,
to market them successfully.


                                       6


<PAGE>   8


Our limited manufacturing capabilities could result in shortages of products
for testing and future sale, and our revenues and profit margin could be
negatively affected.

         While we are producing limited quantities of LJP 394 for clinical
trials, our current facilities are not FDA approved for commercial production of
our potential products. The manufacture of our potential products for clinical
trials and the manufacture of any resulting products for commercial purposes are
subject to certain FDA standards. Substantial capital investment in the
expansion and build-out of our manufacturing facilities will be required to
enable us to manufacture any products in commercial quantities. While we have
initiated the process of obtaining FDA approval for our facilities, we have
never operated an FDA-approved manufacturing facility and may not obtain
necessary approvals. We have limited manufacturing experience, and we may be
unable to successfully transition to commercial production. We may enter into
arrangements with contract manufacturing companies to expand our own production
capacity in order to meet requirements for our products, or to attempt to
improve manufacturing efficiency. If we choose to contract for manufacturing
services and encounter delays or difficulties in establishing relationships with
manufacturers to produce, package and distribute our finished products, the
clinical trials, market introduction and subsequent sales of these products
would be negatively affected by the lack of available products, and our profit
margins and our ability to develop and deliver products on a timely and
competitive basis may be negatively affected.

We lack experience in marketing products for commercial sale and thus may have
difficulty gaining acceptance for our products.

         In order to commercialize any drug candidate approved by the FDA, we
must either develop a marketing and sales force or enter into marketing
arrangements with others. If we cannot do either of these we may have difficulty
generating sales for our products. We currently have no marketing arrangements
with others, and there can be no guarantee that we will be able to enter into
any marketing agreements on favorable terms, or that any such agreements will
result in payments to LJP. To the extent that we enter into co-promotion or
other marketing and sales arrangements with other companies, any revenues that
we may receive will be dependent on the efforts of others. There can be no
guarantee that these efforts will be successful. If we attempt to develop our
own marketing and sales capabilities, we will compete with other companies that
have experienced and well-funded marketing and sales operations. Furthermore, if
we attempt to establish sales and distribution capabilities, we may experience
delays and expenditures and have difficulty in gaining market acceptance for our
drug candidates.

The use of LJP 394 and other potential products in clinical trials, and the sale
of any approved products may expose us to lawsuits resulting from the use of
these products.

         The use and possible sale of LJP 394 and other potential products may
expose us to legal liability and generate negative publicity if claims are made
against us that people were harmed by our products. These claims might be made
directly by consumers, pharmaceutical companies, or others. We maintain $10.0
million of product liability insurance for claims arising from the use of LJP
products in clinical trials. However, coverage is becoming increasingly
expensive, and there can be no guarantee that we will be able to maintain
insurance or that insurance can be acquired at a reasonable cost or in
sufficient amounts to protect us against possible losses. Furthermore, it is
possible that our financial resources would be insufficient to satisfy potential
product liability claims. A successful product liability claim or series of
claims brought could negatively impact our business and financial condition.

Our research and development and operations depend in part on certain key
employees and consultants. Losing these employees or consultants would have
a negative effect on our product development and operations.

         We are highly dependent upon the principal members of our scientific
and management staff, the loss of whose services would delay the achievement of
our research and development objectives. This is because our key personnel,
including Steven Engle, Dr. Andrew Wiseman and Dr. Matthew Linnik, have been
involved in the development of LJP 394 and other drug candidates for several
years and have unique knowledge of our drug candidates and of the technology on
which they are based. Our anticipated growth and expansion into areas requiring
additional expertise, such as clinical trials, government approvals,
manufacturing, and marketing, is expected to place increased demands on our
resources and require the addition of new management personnel as well as the
development of additional expertise by existing management personnel.

         Retaining our current key employees and recruiting additional qualified
scientific personnel to perform research and development work in the future will
also be critical to our success. Because competition for experienced scientists


                                       7
<PAGE>   9


among numerous pharmaceutical and biotechnology companies and research and
academic institutions is intense, we may not be able to attract and retain these
people. If we cannot attract and retain qualified people, our ability to conduct
necessary clinical trials and to develop our products may be negatively affected
because, for instance, the trials may not be conducted properly, or the trials
or our manufacturing of products may be delayed. In addition, we rely upon
consultants and advisors to assist us in formulating our research and
development, clinical, regulatory and manufacturing strategies. All of our
consultants and advisors are employed outside LJP and may have commitments or
consulting or advisory contracts with other entities that may affect their
ability to contribute to our business.


It is possible that we may face environmental liabilities related to certain
hazardous materials used in our operations.


         Due to the nature of our manufacturing processes, we are subject to
stringent federal, state and local laws governing the use, handling and disposal
of certain materials and wastes. It is possible that we may have to incur
significant costs to comply with environmental regulations as our manufacturing
increases to commercial volumes. Our operations may be significantly impacted by
current or future environmental laws because, for instance, our ability to
produce products may be slowed down, which may cause our costs in producing
these products to increase. In our research activities, we use radioactive and
other materials that could be hazardous to human health, safety, or the
environment. These materials and various wastes resulting from their use are
stored at our facility pending ultimate use and disposal. The risk of accidental
injury or contamination from these materials cannot be eliminated. In the event
of such an accident, we could be held liable for any resulting damages, and any
such liability could exceed our resources.

II.  RISK FACTORS RELATED SPECIFICALLY TO OUR STOCK.

Our common stock price is volatile.

         The market price of our common stock has been and is likely to continue
to be highly volatile. Market prices for securities of biotechnology and
pharmaceutical companies, including ours, have historically been highly
volatile, and the market has from time to time experienced significant price and
volume fluctuations that are unrelated to the operating performance of
particular companies. The following factors can have a significant effect on the
market price of our securities:


         o  announcements of technological innovations or new therapeutic
            products by LJP or others,

         o  clinical trial results,

         o  developments concerning agreements with collaborators,

         o  government regulation,

         o  developments in patent or other proprietary rights,

         o  public concern as to the safety of drugs discovered or developed by
            LJP or others,

         o  future sales of substantial amounts of our common stock by existing
            stockholders, and

         o  comments by securities analysts and general market conditions.


The realization of any of the risks described in these "Risk Factors" could have
a negative effect on the market price of our common stock.

In the future, our stock may be removed from listing on the Nasdaq quotation
system and may not qualify for listing on any stock exchange, in which case it
may be difficult to find a market in our stock.

         If our stock is no longer traded on a national trading market it may be
more difficult for you to sell shares that you own, and the price of the stock
may be negatively affected. Currently our securities are traded on the Nasdaq
National Market. Nasdaq has certain continued listing requirements, including a
minimum trading price. Previously, we have received notice from Nasdaq that our
stock price fell below this minimum trading price. While we have since come back
into compliance with this Nasdaq requirement, it is possible that we will fall
out of compliance with this and/or other Nasdaq continued listing criteria



                                       8


<PAGE>   10


at some point in the future. Failure to comply with any one of several Nasdaq
requirements may cause our stock to be removed from listing on Nasdaq. Should
this happen, we may not be able to secure listing on other exchanges or
quotation systems. This would have a negative effect on the price and liquidity
of our stock.

Future sales of our stock by existing stockholders could negatively affect the
market price of our stock and make it more difficult for us to sell stock in the
future.

         Sales of our common stock in the public market, or the perception that
such sales could occur, could result in a drop in the market price of our
securities and make it more difficult for us to complete future equity
financings. In addition to the shares to be sold in this offering, LJP has
outstanding the following shares of common stock:

         o  12,570,000 shares of common stock that have been issued in
            registered offerings and are freely tradable in the public markets.

         o  Approximately 8,900,000 shares of common stock currently eligible
            for resale in the public market pursuant to SEC Rule 144.

         o  An additional 2,000,000 shares of common stock issued to an overseas
            investor pursuant to SEC Regulation S may also be resold.

         o  In addition, an aggregate of 2,592,439 shares of common stock may be
            issued on the exercise of stock options outstanding as of June 30,
            2000 under our various stock option plans at a weighted average
            exercise price of $2.73 per share.

         o  We have in effect or intend to file registration statements under
            the Securities Act registering approximately 4,000,000 shares of
            common stock reserved under our incentive stock option and employee
            stock purchase plans. Approximately 184,000 shares of common stock
            that may be issued on the exercise of outstanding stock options will
            be available for public resale under SEC Rule 144 pursuant to Rule
            701 under the Securities Act.


         o  Abbott has certain registration rights relating to 3,369,604 shares
            of Common Stock that it owns.


         We cannot estimate the number of shares of common stock that may
actually be resold in the public market since this will depend upon the market
price for the common stock, the individual circumstances of the sellers and
other factors. We also have a number of institutional stockholders that own
significant blocks of our common stock. If these stockholders sell large
portions of their holdings in a relatively short time, for liquidity or other
reasons, the market price of our common stock could drop significantly.


Anti-takeover devices and statutes may prevent hostile takeovers or prevent or
delay a change in control of LJP, including transactions that could result in
stockholders receiving a premium for their shares.

         We have in place some anti-takeover devices, including a stockholder
rights plan, that may discourage or deter a potential acquirer from attempting
to gain control of LJP. These devices, plus some of the provisions of the
Delaware General Corporation Law, may have the effect of deterring hostile
takeovers or delaying or preventing changes in the control or management of LJP,
including transactions in which stockholders might otherwise receive a premium
for their shares over then-current market prices. The existence of the
anti-takeover protections could have a negative effect on the price of our
stock.






                                       9
<PAGE>   11


         Another anti-takeover device provides for a board of directors that is
separated into three classes, with their terms in office staggered over three
year periods. This has the effect of delaying a change in control of the Board
of Directors without the cooperation of the incumbent board. In addition, our
bylaws do not allow stockholders to call a special meeting of stockholders,
require stockholders to give written notice of any proposal or director
nomination to us within a certain period of time prior to the stockholder annual
meeting, and establish certain qualifications for a person to be elected or
appointed to the Board of Directors during the pendency of certain business
combination transactions.

         We may also issue shares of preferred stock without stockholder
approval and upon terms that our Board of Directors may determine in the future.
The issuance of preferred stock could have the effect of making it more
difficult for a third party to acquire a majority of our outstanding stock, and
the holders of such preferred stock could have voting, dividend, liquidation and
other rights superior to those of holders of the common stock.

We do not pay dividends and this may negatively affect the price of our stock.

         We have not paid any cash dividends since our inception and do not
anticipate paying any cash dividends in the foreseeable future. The future price
of our common stock may be depressed by the fact that we have not paid
dividends.


                                 USE OF PROCEEDS

         We will not receive any proceeds from the sale of the shares of common
stock by the selling stockholders.

                              SELLING STOCKHOLDERS


         In a series of private transactions completed on July 24, 2000, we
issued a total of 4,800,00 shares of our common stock to the stockholders listed
below. The selling stockholders may from time to time offer and sell pursuant to
this prospectus any or all of 4,800,000 shares of our common stock. The
following table describes, as of July 24, 2000, the number of shares of our
common stock that each selling stockholder beneficially owns. The term "selling
stockholders" includes the holders listed below and their transferees, pledgees,
donees or other successors. We have prepared this table based upon information
furnished to us by or on behalf of the selling stockholders.

         The selling stockholders confirmed at the time they acquired the shares
listed below that they acquired the shares for investment purposes only and not
with a view toward their resale, and acknowledged the existence of restrictions
on resale that apply to these shares. This offering relates only to the sale of
shares held or to be held by the selling stockholders named in the following
table. Since the date on which they provided us with the information below, the
selling stockholders may have sold, transferred or otherwise disposed of some or
all of their shares of our common stock in transactions exempt from the
Securities Act's registration requirements.


<TABLE>
<CAPTION>
                                                    Beneficial Ownership                    Beneficial Ownership
                                                      Prior to Offering                        After Offering
                                              --------------------------------------      -------------------------
                                                Number        Percent    Shares            Number         Percent
                                                  of            of        to be              of              of
Name of Beneficial Owner                        Shares        Class(1)   Sold (2)         Shares(2)      Class(2)
------------------------                      ---------       --------  ---------         ---------      --------
<S>                                           <C>             <C>       <C>               <C>            <C>
State of Wisconsin Investment Board           4,114,300        14.0%    1,750,000         2,364,300        8.1%

DWS Investments GmbH                          2,400,000         8.2%    1,200,000         1,200,000        4.1%

Alta BioPharma Partners, LP                   1,193,445         4.1%      279,714           913,731        3.1%

La Jolla Chase Partners (Alta Bio), LLC         681,571         2.3%      159,743           521,828        1.8%

Special Situations Fund III, LP                 507,000         1.7%      270,000           237,000           *

HSBC Bank PLC                                   450,000         1.5%      450,000                --          --

Lares & Co.                                     350,000         1.2%      350,000                --          --

Special Situations Private Equity Fund, LP      264,100            *      200,000            64,100           *

Special Situations Cayman Fund, LP              168,900            *       90,000            78,900           *

Chase Equity Associates, LP                      55,000            *       40,000            15,000           *

Alta Embarcadero BioPharma, LLC                  44,984            *       10,543            34,441           *
</TABLE>


                                       10


<PAGE>   12

---------------
 *  Less than 1%

(1) Computed based on 29,288,361 shares of common stock outstanding as of
    July 24, 2000.

(2) Assumes all the shares of common stock that may be offered hereunder are
    sold.


         The information regarding the selling stockholders may change from time
to time. If required, we will describe these changes in one or more prospectus
supplements.


                              PLAN OF DISTRIBUTION


         The selling stockholders can use this prospectus to sell the shares at
any time while the prospectus is in effect, unless we have notified the selling
stockholders that the prospectus is not available at that particular time. The
selling stockholders will determine if, when and how they will sell the shares
they own. Any sales may occur in one or more of the following types of
transactions (including block transactions):


         o  transactions on the Nasdaq National Market or any other organized
            market or quotation system where the shares may be traded,

         o  privately negotiated transactions between a selling stockholder and
            a purchaser, or

         o  transactions effected with or through a broker-dealer acting as
            either agent or principal.


         These transactions may involve the transfer of the shares upon exercise
or settlement of put or call options, or the delivery of the shares to replace
shares that were previously borrowed from another stockholder or a combination
of such methods. If a broker-dealer is used in the sale of shares, that person
may solicit potential purchasers. The shares may also be transferred as a gift
or as a result of a pledge, or may be sold to a broker-dealer acting as
principal. These persons may then sell the shares to another person, either
directly or through another broker-dealer, subject to compliance with the
requirements of the Securities Act.

         The price at which sales of the shares occur may be based on market
prices or may be negotiated between the parties, and the consideration may be
cash or another form negotiated between the parties. Broker-dealers acting as
agents or principals may be paid compensation in the form of discounts,
concessions or commissions from the selling stockholder and/or from the
purchasers of the shares, or both. Brokers or dealers may be deemed to be
"underwriters" within the meaning of the Securities Act. Any profits on the
resale of shares by a broker-dealer acting as principal might be deemed to be
underwriting discounts or commissions under the Securities Act. Discounts,
concessions, commissions and similar selling expenses, if any, that can be
attributed to the sale of shares will be paid by the selling stockholder and/or
the purchasers. We have agreed to pay certain of the costs, expenses and fees of
preparing, filing and maintaining this prospectus and the registration statement
of which this prospectus is a part, but we will not receive any proceeds from
sale of these shares. The selling stockholders may agree to indemnify any agent,
dealer or broker-dealer that participates in transactions involving sales of the
shares if liabilities are imposed on it under the Securities Act.


         The selling stockholders have advised us that they have not entered
into any agreements, understandings or arrangements with any underwriters or
broker-dealers regarding the sale of their shares, nor is there an underwriter
or coordinating broker acting in connection with a proposed sale of shares by
any selling stockholder. If we are notified by any selling stockholder that any
material arrangement has been entered into with a broker-dealer for the sale of
shares, if required, we will file a supplement to this prospectus.


                                       11


<PAGE>   13

         If the selling stockholders use this prospectus for any sale of the
shares, they will be subject to the prospectus delivery requirements of the
Securities Act. For transactions effected on or through the Nasdaq, those
requirements may be satisfied by our delivery of copies of this prospectus to
the Nasdaq in compliance with Securities Act Rule 153. Instead of using this
prospectus for any sale of the shares, a selling stockholder may resell shares
in compliance with the criteria and requirements of Securities Act Rule 144.

         The anti-manipulation rules of Regulation M under the Securities
Exchange Act of 1934 may apply to sales of our common stock and activities of
the selling stockholder.

                               WHERE YOU CAN FIND
                                MORE INFORMATION

         We file periodic reports, proxy statements and other information with
the Securities and Exchange Commission. You may inspect and copy these reports
and other information at the SEC's public reference facilities in Washington,
D.C. (located at 450 Fifth Street, N.W., Washington, D.C. 20549), Chicago
(located at Northwestern Atrium Center, 500 West Madison Street, Suite 1400,
Chicago, Illinois 60661) and New York (located at Seven World Trade Center, 13th
Floor, New York, New York 10048). You can also obtain copies of these materials
from the SEC's public reference section (located at 450 Fifth Street, N.W.,
Washington, D.C. 20549) at prescribed rates. Please call the SEC at
1-800-SEC-0300 for further information about the public reference rooms. The SEC
also maintains a site on the World Wide Web at http://www.sec.gov. This site
contains reports, proxy and information statements and other information about
registrants that file electronically with the SEC.

         The SEC permits us to "incorporate by reference" the information and
reports we file with it. This means that we can disclose important information
to you by referring to another document. The information that we incorporate by
reference is considered to be part of this prospectus, and later information
that we file with the SEC automatically updates and supersedes this information.
Specifically, we incorporate by reference:

         1. Our Annual Report on Form 10-K and Form 10-K/A for the fiscal year
            ended December 31, 1999;

         2. Our Quarterly Reports on Form 10-Q for the quarters ended March 31,
            2000 and June 30, 2000;

         3. Our Current Report on Form 8-K dated April 18, 2000;

         4. Our Proxy Statement dated April 10, 2000;

         5. The description of our common stock contained in our Registration
            Statements on Form 8-A, filed on June 2, 1994 and December 4, 1998;
            and

         6. All documents we file with the SEC pursuant to Sections 13(a),
            13(c), 14 and 15(d) of the Exchange Act after the date of this
            prospectus and prior to the termination of the offering of the
            shares offered by this prospectus.


         We have also filed a registration statement on Form S-3 with the SEC.
This prospectus does not contain all of the information set forth in the
registration statement. You should read the registration statement for further
information about us and our common stock.


         We will provide a copy of these filings to each person, including any
beneficial owner, to whom we deliver this prospectus, upon written or oral
request. You may request a copy of these filings at no cost by writing or
telephoning us at the following address:

                               Corporate Secretary
                         La Jolla Pharmaceutical Company
                             6455 Nancy Ridge Drive
                           San Diego, California 92121
                                 (858) 452-6600


                                       12


<PAGE>   14

         You should rely only on the information contained in this prospectus.
We have authorized no one to provide you with different information. We are not
making an offer of these securities in any state where the offer is not
permitted. You should not assume that the information in this prospectus is
accurate as of any date other than the date on the front of this prospectus.

                           FORWARD-LOOKING STATEMENTS

         We have made forward-looking statements in this prospectus that are
based on our management's beliefs and assumptions and on information currently
available to our management. Forward-looking statements include information
concerning our possible or assumed future results of operations and statements
preceded by, followed by or that include the words "believes," "expects,"
"anticipates," "intends," "plans," "estimates" or similar expressions.

         Forward-looking statements involve risks, uncertainties and
assumptions. Actual results may differ materially from those expressed in these
forward-looking statements. You are cautioned not to put undue reliance on any
forward-looking statements. Except as may be required by law, we do not have any
intention or obligation to update forward-looking statements after we distribute
this prospectus. These statements appear in a number of places in this
prospectus and include statements regarding our intentions, plans, strategies,
beliefs or current expectations and those of our directors or our officers with
respect to, among other things:


         o  our financial prospects,

         o  our financing plans,

         o  trends affecting our financial condition or operating results,

         o  our strategies for growth, operations, and product development and
            commercialization, and

         o  conditions or trends in or factors affecting the biotechnology
            industry.

         You should understand that a number of factors could cause our results
to differ materially from those expressed in the forward-looking statements. The
information incorporated by reference or provided in this prospectus identifies
important factors that could cause these differences. Those factors include,
among others, the high cost and uncertainty of technology and drug development,
which can result in loss of profitability and long delays in getting products to
market.


                                  LEGAL MATTERS

         The validity of the shares of common stock covered by this prospectus
was passed upon by Gibson, Dunn & Crutcher LLP, Irvine, California.

                                     EXPERTS


         The financial statements of La Jolla Pharmaceutical Company
incorporated by reference in La Jolla Pharmaceutical Company's Annual Report
(Form 10-K/A) for the year ended December 31, 1999, have been audited by Ernst &
Young LLP, independent auditors, as set forth in their report thereon and
incorporated herein by reference. These financial statements are incorporated
herein by reference in reliance upon such report given on the authority of such
firm as experts in accounting and auditing.



                                       13

<PAGE>   15

================================================================================

         NO PERSON HAS BEEN AUTHORIZED IN CONNECTION WITH ANY OFFERING MADE
UNDER THIS PROSPECTUS TO GIVE ANY INFORMATION OR TO MAKE ANY REPRESENTATIONS
OTHER THAN THOSE CONTAINED IN THIS PROSPECTUS. IF GIVEN OR MADE, SUCH
INFORMATION OR REPRESENTATIONS MUST NOT BE RELIED UPON AS HAVING BEEN AUTHORIZED
BY US OR THE SELLING STOCKHOLDERS. NEITHER THE DELIVERY OF THIS PROSPECTUS NOR
ANY SALE MADE UNDER THIS PROSPECTUS WILL, UNDER ANY CIRCUMSTANCES, IMPLY THAT
THERE HAS BEEN NO CHANGE IN OUR AFFAIRS OR THAT THE INFORMATION IN THIS
PROSPECTUS IS CORRECT AS OF ANY TIME SUBSEQUENT TO THE DATE AS OF WHICH THE
INFORMATION IS GIVEN. THIS PROSPECTUS DOES NOT CONSTITUTE AN OFFER TO SELL OR
THE SOLICITATION OF ANY OFFER TO BUY ANY OF THE SECURITIES OFFERED UNDER THIS
PROSPECTUS TO ANYONE IN ANY JURISDICTION IN WHICH THE OFFER OR SOLICITATION IS
NOT AUTHORIZED OR IN WHICH THE PERSON MAKING THE OFFER OR SOLICITATION IS NOT
QUALIFIED TO DO SO OR TO ANYONE TO WHOM IT IS UNLAWFUL TO MAKE THE OFFER OR
SOLICITATION.

                                ----------------


                                TABLE OF CONTENTS

Risk Factors........................................2
Use of Proceeds....................................10
Selling Stockholders...............................10
Plan of Distribution...............................11
Where You Can Find More Information................12
Forward-Looking Statements.........................13
Legal Matters......................................13
Independent Experts................................13


================================================================================


================================================================================



                                   [LJP LOGO]



                                4,800,000 SHARES
                                  COMMON STOCK



                                ----------------
                                   PROSPECTUS
                                ----------------



                               SEPTEMBER 1, 2000


================================================================================

<PAGE>   16

                 PART II. INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION

         The following table sets forth all expenses payable by us in connection
with the offering of our common stock being registered hereby. All amounts are
estimated except the SEC registration fee.

         SEC Registration Fee....................................    $ 8,440
         Printing Expenses.......................................    $    --
         Legal Fees and Expenses.................................    $15,000
         Accounting Fees and Expenses............................    $10,000
         Miscellaneous...........................................    $20,000
                                                                     -------
              Total..............................................    $53,440
                                                                     =======

ITEM 15. INDEMNIFICATION OF OFFICERS AND DIRECTORS

         Section 145(a) of the General Corporation Law of the State of Delaware
(the "DGCL") provides that a Delaware corporation may indemnify any person who
was or is a party or is threatened to be made a party to any threatened, pending
or completed action, suit or proceeding, whether civil, criminal, administrative
or investigative, other than an action by or in the right of the corporation, by
reason of the fact that such person is or was a director, officer, employee or
agent of the corporation or is or was serving at the request of the corporation
as a director, officer, employee or agent of another corporation or enterprise,
against expenses, judgments, fines and amounts paid in settlement actually and
reasonably incurred by such person in connection with such action, suit or
proceeding if he or she acted in good faith and in a manner he or she reasonably
believed to be in or not opposed to the best interests of the corporation, and,
with respect to any criminal action or proceeding, had no cause to believe his
or her conduct was unlawful.

         Section 145(b) of the DGCL provides that a Delaware corporation may
indemnify any person who was or is a party or is threatened to be made a party
to any threatened, pending or completed action or suit by or in the right of
corporation to procure a judgment in its favor by reason of the fact that such
person acted in any of the capacities set forth above, against expenses actually
and reasonably incurred by such person in connection with the defense or
settlement of such action or suit if he or she acted under similar standards to
those set forth above, except that no indemnification may be made in respect to
any claim, issue or matter as to which such person shall have been adjudged to
be liable to the corporation unless and only to the extent that the court in
which such action or suit was brought shall determine that despite the
adjudication of liability, but in view of all the circumstances of the case,
such person is fairly and reasonably entitled to be indemnified for such
expenses which the court shall deem proper.

         Section 145 of the DGCL further provides that to the extent a director
or officer of a corporation has been successful in the defense of any action,
suit or proceeding referred to in subsection (a) and (b) of Section 145 or in
the defense of any claim, issue or matter therein, he or she shall be
indemnified against expenses actually and reasonably incurred by him or her in
connection therewith; that indemnification provided for by Section 145 shall not
be deemed exclusive of any other rights to which the indemnified party may be
entitled; and that the corporation may purchase and maintain insurance on behalf
of a director or officer of the corporation against any liability asserted
against such officer or director and incurred by him or her in any such capacity
or arising out of his or her status as such, whether or not the corporation
would have the power to indemnify him or her against such liabilities under
Section 145.

         As permitted by Section 102(b)(7) of the DGCL our certificate of
incorporation provides that a director shall not be liable to us or our
stockholders for monetary damages for breach of fiduciary duty as a director.
However, such provision does not eliminate or limit the liability of a director
for acts or omissions not in good faith or for breaching his or her duty of
loyalty, engaging in intentional misconduct or knowingly violating the law,
paying a dividend or approving a stock repurchase which was illegal, or
obtaining an improper personal benefit. A


                                      II-1


<PAGE>   17

provision of this type has no effect on the availability of equitable remedies,
such as injunction or rescission, for breach of fiduciary duty.

         Our bylaws require that directors and officers be indemnified to the
maximum extent permitted by Delaware law.

         The Company has entered into indemnity agreements with each of its
directors and executive officers. These indemnity agreements require that the
Company pay on behalf of each director and officer party thereto any amount that
he or she is or becomes legally obligated to pay because of any claim or claims
made against him or her because of any act or omission or neglect or breach of
duty, including any actual or alleged error or misstatement or misleading
statement, which he or she commits or suffers while acting in his or her
capacity as a director and/or officer of the Company and solely because of his
or her being a director and/or officer. Under the General Corporation Law,
absent such an indemnity agreement, indemnification of a director or officer is
discretionary rather than mandatory (except in the case of a proceeding in which
a director or officer is successful on the merits). Consistent with the
Company's Bylaw provision on the subject, the indemnity agreements require the
Company to make prompt payment of defense and investigation costs and expenses
at the request of the director or officer in advance of indemnification,
provided that the recipient undertakes to repay the amounts if it is ultimately
determined that he or she is not entitled to indemnification for such expenses
and provided further that such advance shall not be made if it is determined
that the director or officer acted in bad faith or deliberately breached his or
her duty to the Company or its stockholders and, as a result, it is more likely
than not that it will ultimately be determined that he or she is not entitled to
indemnification under the terms of the indemnity agreement. The indemnity
agreements make the advance of litigation expenses mandatory absent a special
determination to the contrary, whereas under the General Corporation Law absent
such an indemnity agreement, such advance would be discretionary. Under the
indemnity agreement, the director or officer is permitted to petition the court
to seek recovery of amounts due under the indemnity agreement and to recover the
expenses of seeking such recovery if he or she is successful. Without the
indemnity agreement, the Company would not be required to pay or reimburse the
director or officer for his or her expenses in seeking indemnification recovery
against the Company. By the terms of the indemnity agreement, its benefits are
not available if the director or officer has other indemnification or insurance
coverage for the subject claim or, with respect to the matters giving rise to
the claim, (i) received a personal benefit, (ii) violated Section 16(b) of the
Securities Exchange Act of 1934 or analogous provisions of law, or (iii)
committed certain acts of dishonesty. Absent the indemnity agreement,
indemnification that might be made available to directors and officers could be
changed by amendments to the Company's Certificate of Incorporation or Bylaws.

         The Company has a policy of directors and officers liability insurance
that insures the Company and its directors and officers against damages,
settlements, and defense costs under certain circumstances.

ITEM 16. EXHIBITS

         The following exhibits are filed herewith or incorporated by reference:

   EXHIBIT
   NUMBER                       DESCRIPTION OF EXHIBIT
   -------                      ----------------------
    4.1    Amended and Restated Certificate of Incorporation of the Company (1)

    4.2    Amended and Restated Bylaws of the Company (2)

    4.3    Form of Common Stock Certificate (3)

    4.4    Rights Agreement dated December 3, 1998 between the Company
           and American Stock Transfer & Trust Company (4)

    4.5    Certificate of Designation, Preferences and Rights of Series A
           Junior Participating Preferred Stock of the Company (5)


    5.1    Opinion of Gibson, Dunn & Crutcher LLP as to legality of the
           securities registered hereby (6)


   23.1    Consent of Gibson, Dunn & Crutcher LLP (included in Exhibit 5.1)

   23.2    Consent of Ernst & Young LLP, independent auditors

   24.1    Power of Attorney (contained on signature page of this document)


                                      II-2


<PAGE>   18

-------------

(1)  Incorporated by reference to our Quarterly Report on Form 10-Q, Exhibit
     3.3, filed November 15, 1999.

(2)  Incorporated by reference to our Quarterly Report on Form 10-Q, Exhibit
     3.2, filed November 15, 1999.

(3)  Incorporated by reference to Amendment No. 4 to our Registration Statement
     on Form S-1, Exhibit 4.1, filed June 2, 1994 (Registration No. 33-76480).

(4)  Previously filed with the Company's Registration Statement on Form 8-A (No.
     000-24274) as filed with the Securities and Exchange Commission on December
     4, 1998.

(5)  Incorporated by reference to our Quarterly report on Form 10-Q, Exhibit
     4.1, filed August 13, 1999.


(6)  Previously filed with this Registration Statement on August 4, 2000.


ITEM 17. UNDERTAKINGS

The undersigned registrant hereby undertakes:

            (1) To file, during any period in which offers or sales are being
         made, a post-effective amendment to this registration statement:

                (i)    To include any prospectus required by Section 10(a)(3) of
                       the Securities Act;

                (ii)   To reflect in the prospectus any facts or events arising
                       after the effective date of the registration statement
                       (or the most recent post-effective amendment thereof)
                       which, individually or in the aggregate, represent a
                       fundamental change in the information set forth in the
                       registration statement;

                (iii)  To include any material information with respect to the
                       plan of distribution not previously disclosed in the
                       registration statement or any material change to such
                       information in the registration statement;

provided, however, that paragraphs (1)(i) and (1)(ii) do not apply if the
information required to be included in a post-effective amendment by those
paragraphs is contained in periodic reports filed with or furnished to the
Securities Exchange Commission by the registrant pursuant to Section 13 or
Section 15(d) of the Securities Exchange Act that are incorporated by reference
in the registration statement.

            (2) That, for the purpose of determining any liability under the
         Securities Act, each post-effective amendment shall be deemed to be a
         new registration statement relating to the securities offered herein,
         and the offering of such securities at that time shall be deemed to be
         the initial bona fide offering thereof.

            (3) To remove from registration by means of a post-effective
         amendment any of the securities being registered which remain unsold at
         the termination of the offering.

         The undersigned registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act, each filing of the
registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Securities Exchange Act that is incorporated by reference in the registration
statement shall be deemed to be a new registration statement relating to the
securities offered herein, and the offering of such securities at that time
shall be deemed to be the initial bona fide offering thereof.

         Insofar as indemnification for liabilities arising under the Securities
Act may be permitted to directors, officers and controlling persons of the
registrant, the registrant has been advised that in the opinion of the
Securities and Exchange Commission such indemnification is against public policy
as expressed in the Securities Act and is,


                                      II-3


<PAGE>   19

therefore, unenforceable. In the event that a claim for indemnification against
such liabilities (other than the payment by the registrant of expenses incurred
or paid by a director, officer or controlling person of the registrant in the
successful defense of any action, suit or proceeding) is asserted by such
director, officer or controlling person in connection with the securities being
registered, the registrant will, unless in the opinion of counsel the matter has
been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question whether such indemnification by it is against public
policy as expressed in the Securities Act and will be governed by the final
adjudication of such issue.



                                      II-4

<PAGE>   20

                                   SIGNATURES


         Pursuant to the requirements of the Securities Act of 1933, as amended,
I certify that I have reasonable grounds to believe that La Jolla Pharmaceutical
Company meets all of the requirements for filing on Form S-3 and has duly caused
this Registration Statement to be signed on its behalf by the undersigned,
thereunto duly authorized, in the City of Irvine, State of California, on
September 1, 2000.


                                        LA JOLLA PHARMACEUTICAL COMPANY

                                        By: /s/ Steven B. Engle*
                                            ------------------------------------
                                            Steven B. Engle
                                            Chairman and Chief Executive Officer

                                POWER OF ATTORNEY

         Each person whose signature appears below constitutes and appoints
Steven B. Engle and Gail A. Sloan his or her true and lawful attorneys-in-fact
and agents, each acting alone, with full powers of substitution and
resubstitution, for him or her and in his or her name, place and stead, in any
and all capacities, to sign any and all amendments (including post-effective
amendments) to this Registration Statement and to file the same, with all
exhibits thereto, and other documents in connection therewith, with the
Securities and Exchange Commission, granting unto said attorneys-in-fact and
agents, each acting alone, full power and authority to do and perform each and
every act and thing requisite and necessary to be done in and about the
premises, as full to all intents and purposes as he or she might or could do in
person, hereby ratifying and confirming all that said attorneys-in-fact and
agents, each acting alone, or his substitute or substitutes, may lawfully do or
cause to be done by virtue hereof.

         Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.


<TABLE>
<CAPTION>

    NAME AND SIGNATURE                               TITLE                                   DATE
    ------------------                               -----                                   ----
<S>                                         <C>                                         <C>
/s/ Steven B. Engle*                        Chairman of the Board, Chief Executive      September 1, 2000
------------------------------------        Officer, President and Director
    Steven B. Engle                         (Principal Executive Officer)


/s/ Gail A. Sloan                           Secretary and Controller (Principal         September 1, 2000
------------------------------------        Financial and Accounting Officer)
    Gail A. Sloan


/s/ Thomas H. Adams, Ph.D.*                 Director                                    September 1, 2000
------------------------------------
    Thomas H. Adams, Ph.D.


/s/ William E. Engbers*                     Director                                    September 1, 2000
------------------------------------
    William E. Engbers


/s/ Robert A. Fildes, Ph.D.*                Director                                    September 1, 2000
------------------------------------
    Robert A. Fildes, Ph.D.


/s/ Stephen M. Martin*                      Director                                    September 1, 2000
------------------------------------
    Stephen M. Martin


/s/ Leigh Thompson, M.D., Ph.D.*            Director                                    September 1, 2000
------------------------------------
    W. Leigh Thompson, M.D., Ph.D.

* By power-of-attorney
</TABLE>



                                      II-5

<PAGE>   21

                                  EXHIBIT INDEX

EXHIBIT
NUMBER                 DESCRIPTION OF EXHIBIT
-------                ----------------------
 4.1     Amended and Restated Certificate of Incorporation of the Company (1)

 4.2     Amended and Restated Bylaws of the Company (2)

 4.3     Form of Common Stock Certificate (3)

 4.4     Rights Agreement dated December 3, 1998 between the Company
         and American Stock Transfer & Trust Company (4)

 4.5     Certificate of Designation, Preferences and Rights of Series A
         Junior Participating Preferred Stock of the Company (5)


 5.1     Opinion of Gibson, Dunn & Crutcher LLP as to legality of the
         securities registered hereby (6)


23.1     Consent of Gibson, Dunn & Crutcher LLP (included in Exhibit 5.1)

23.2     Consent of Ernst & Young LLP, independent auditors

24.1     Power of Attorney (contained on signature page of this document)

-------------
(1)  Incorporated by reference to our Quarterly Report on Form 10-Q, Exhibit
     3.3, filed November 15, 1999.

(2)  Incorporated by reference to our Quarterly Report on Form 10-Q, Exhibit
     3.2, filed November 15, 1999.

(3)  Incorporated by reference to Amendment No. 4 to our Registration Statement
     on Form S-1, Exhibit 4.1, filed June 2, 1994 (Registration No. 33-76480).

(4)  Previously filed with the Company's Registration Statement on Form 8-A (No.
     000-24274) as filed with the Securities and Exchange Commission on December
     4, 1998.

(5)  Incorporated by reference to our Quarterly report on Form 10-Q, Exhibit
     4.1, filed August 13, 1999.


(6)  Previously filed with this Registration Statement on August 4, 2000.



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