HOLLIS EDEN PHARMACEUTICALS INC /DE/
S-3, 1998-12-24
PHARMACEUTICAL PREPARATIONS
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<PAGE>   1
 
   AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON DECEMBER 24, 1998
 
                                                     REGISTRATION NO.

===============================================================================
 
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                            ------------------------
 
                                    FORM S-3
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933

                            ------------------------
 
                       HOLLIS-EDEN PHARMACEUTICALS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)
 
<TABLE>
<S>                                                 <C>
                     DELAWARE                                           13-3697002
 (STATE OR OTHER JURISDICTION OF INCORPORATION OR         (I.R.S. EMPLOYER IDENTIFICATION NUMBER)
                   ORGANIZATION)
</TABLE>
 
                         9333 GENESEE AVENUE, SUITE 110
                          SAN DIEGO, CALIFORNIA 92121
                                 (619) 587-9333
  (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
                   REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)
 
                               RICHARD B. HOLLIS
               CHAIRMAN OF THE BOARD AND CHIEF EXECUTIVE OFFICER
                       HOLLIS-EDEN PHARMACEUTICALS, INC.
                         9333 GENESEE AVENUE, SUITE 110
                          SAN DIEGO, CALIFORNIA 92121
                                 (619) 587-9333
 (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
                             OF AGENT FOR SERVICE)
 
                                   COPIES TO:
                             ERIC J. LOUMEAU, ESQ.
                               COOLEY GODWARD LLP
                        4365 EXECUTIVE DRIVE, SUITE 1100
                              SAN DIEGO, CA 92121
                                 (619) 550-6000
 
        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
     From time to time after this Registration Statement becomes effective.
 
    If the only securities being registered on this Form are being 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 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>
==============================================================================================================================
                                                           PROPOSED MAXIMUM        PROPOSED MAXIMUM
      TITLE OF CLASS OF               AMOUNT TO             OFFERING PRICE            AGGREGATE               AMOUNT OF
 SECURITIES TO BE REGISTERED        BE REGISTERED            PER SHARE(1)         OFFERING PRICE(1)        REGISTRATION FEE
- ------------------------------------------------------------------------------------------------------------------------------
<S>                                    <C>                      <C>                  <C>                        <C>
Common Stock, $.01 par
  value.......................         931,373                  $15.50               $14,436,282                $4,013
==============================================================================================================================
</TABLE>
 
(1) Estimated solely for the purpose of calculating the amount of the
    registration fee pursuant to Rule 457(c) of the Securities Act of 1933. The
    price per share and aggregate offering price are based upon the average of
    the high and low sales price of Hollis-Eden's common stock on December 23,
    1998 as reported on the Nasdaq National Market. It is not known how many
    shares will be purchased under this registration statement or at what price
    such shares will be purchased.
 
    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 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
 
                 SUBJECT TO COMPLETION, DATED DECEMBER 24, 1998
 
                                 931,373 Shares
 
                       HOLLIS-EDEN PHARMACEUTICALS, INC.
 
                                  Common Stock
 
                            ------------------------
 
Selling stockholders identified in this prospectus are selling 931,373 shares of
Hollis-Eden Pharmaceuticals, Inc. common stock. Hollis-Eden will not receive any
of the proceeds from the sale of shares by the selling stockholders.
Hollis-Eden's common stock is listed on the Nasdaq National Market under the
symbol "HEPH." The closing sale price of the common stock, as reported on the
Nasdaq National Market on December 23, 1998, was $15.5625 per share.
 
The selling stockholders may sell the shares of common stock described in this
prospectus in public or private transactions, on or off the Nasdaq National
Market, at prevailing market prices, or at privately negotiated prices. The
selling stockholders may sell shares directly to purchasers or through brokers
or dealers. Brokers or dealers may receive compensation in the form of
discounts, concessions or commissions from the selling stockholders. More
information is provided in the section entitled "Plan of Distribution."
 
INVESTING IN THE COMMON STOCK INVOLVES A HIGH DEGREE OF RISK. SEE "RISK
FACTORS," BEGINNING ON PAGE 4.
 
NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR DETERMINED IF THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.
 
The date of this prospectus is January   , 1999.
 
THE INFORMATION CONTAINED IN THIS PROSPECTUS IS NOT COMPLETE AND MAY BE CHANGED.
THESE SECURITIES MAY NOT BE SOLD TO YOU 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.
<PAGE>   3
 
                       WHERE YOU CAN GET MORE INFORMATION
 
We are a reporting company and file annual, quarterly and current reports, proxy
statements and other information with the SEC. You may read and copy these
reports, proxy statements and other information at the SEC's public reference
rooms in Washington, D.C., New York, NY and Chicago, IL. You can request copies
of these documents by writing to the SEC and paying a fee for the copying cost.
Please call the SEC at 1-800-SEC-0330 for more information about the operation
of the public reference rooms. Our SEC filings are also available at the SEC's
Web site at "http://www.sec.gov". In addition, you can read and copy our SEC
filings at the office of the National Association of Securities Dealers, Inc. at
1735 K Street, Washington, D.C. 20006.
 
The SEC allows us to "incorporate by reference" information that we file with
them, which means that we can disclose important information to you by referring
you to those documents. The information incorporated by reference is an
important part of this prospectus, and information that we file later with the
SEC will automatically update and supersede this information. We incorporate by
reference the documents listed below and any future filings we will make with
the SEC under Section 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act
of 1934:
 
     - Annual Report on Form 10-K for the year ended December 31, 1997;
 
     - Quarterly Reports on Form 10-Q for the quarters ended March 31, 1998,
       June 30, 1998 and September 30, 1998;
 
     - Proxy Statement for the 1998 Annual Meeting of Stockholders;
 
     - Current Report on Form 8-K filed May 7, 1998; and
 
     - Hollis-Eden's registration statement on Form S-4, as amended, which
       includes a description of Hollis-Eden's common stock.
 
You may request a copy of these filings at no cost, by writing or telephoning us
at the following address or telephone number:
 
          Hollis-Eden Pharmaceuticals, Inc.
          9333 Genesee Avenue, Suite 110
          San Diego, CA 92121
          Attn: Vice President-Controller
          (619) 587-9333
 
This prospectus is part of a larger registration statement we filed with the
SEC. You should rely only on the information incorporated by reference or
provided in this prospectus. We have not authorized anyone else 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 the document.
 
                                        2
<PAGE>   4
 
                                  THE COMPANY
 
Except for historical information, the information contained in this prospectus
and in our SEC reports are "forward looking" statements about our expected
future business and performance. Our actual operating results and financial
performance may prove to be very different from what we might have predicted as
of the date of this prospectus. The risks described below address some of the
factors that may affect our future operating results and financial performance.
 
Hollis-Eden is a pharmaceutical company in the development stage. We intend to
discover, develop and commercialize products for the treatment of a number of
targeted disease states caused by viral, bacterial, parasitic or fungal
infections, including HIV/AIDS, hepatitis B and C, and malaria. We have three
technology platforms, the first based on cellular energy regulation, the second
on a unique immune system modulation technology, and the third on biochemical
synthesis regulators. We believe that certain of our drug candidates may provide
the first long-term treatment of HIV without the development of viral strain
resistance to the drugs' effectiveness, significant toxicity or severe side
effects.
 
Hollis-Eden's executive offices are located at 9333 Genesee Avenue, Suite 110,
San Diego, California 92121, telephone number (619) 587-9333.
 
                                USE OF PROCEEDS
 
Hollis-Eden will not receive any proceeds from the sale of the shares of common
stock offered by the selling stockholders.
 
                                        3
<PAGE>   5
 
                                  RISK FACTORS
 
An investment in the shares being offered hereby involves a high degree of risk.
In deciding whether to purchase shares of our common stock, you should carefully
consider the following risk factors, in addition to other information contained
in this prospectus, in our most recent quarterly report on Form 10-Q, in our
most recent annual report on Form 10-K, and in any other documents incorporated
by reference into this prospectus from our other SEC filings.
 
DEPENDENCE ON NEW PRODUCTS AND FDA APPROVAL
 
Our principal development efforts are currently centered around two drug
candidates licensed to us which we believe show promise for the treatment and
prevention of HIV/ AIDS. However, all of our drug candidates will require Food
and Drug Administration ("FDA") and foreign government approvals before they can
be commercialized. Neither HE2000 nor any of our other drug candidates have been
approved for commercial sale. While limited clinical trials of HE2000 have to
date produced favorable results, significant additional trials are required, and
we may not be able to demonstrate that this drug candidate is safe or effective.
We have never commercially introduced a product, and we cannot guarantee that
any of our product candidates will obtain required governmental approvals or
that we can successfully commercialize any products.
 
EARLY STAGE OF PRODUCT DEVELOPMENT AND SUBSTANTIAL OPERATING LOSSES
 
We have experienced significant operating losses to date because of the
substantial expenses we have incurred to acquire and fund development of our
drug candidates. We have never had operating revenues. Our accumulated deficit
was $11.4 million through September 30, 1998. We expect to incur significant
additional operating losses over the next several years as we fund development,
clinical testing and other expenses of seeking FDA approval. Many of our
research and development programs are at an early stage. Potential drug
candidates are subject to inherent risks of failure. These risks include the
possibilities that no drug candidate will be found safe or effective, meet
applicable regulatory standards or receive the necessary regulatory clearances.
Even safe and effective drug candidates may never be developed into commercially
successful drugs. There may be delays in receipt of regulatory approvals. The
drugs could be uneconomical to manufacture or produce on a large scale. The
drugs may not achieve customer acceptance. The proprietary rights of others
could stop us from being able to market the drugs, or third parties could market
superior or equivalent drugs. If we were unable to develop safe, commercially
viable drugs, it would have a material adverse effect on our business, financial
condition and results of operations. Our ability to achieve profitable
operations will depend on our ability to obtain regulatory approvals for our
drug candidates, our ability to enter into collaboration agreements, and our
ability to commercialize a drug candidate. We cannot assure you that we will
ever operate profitably.
 
PATENTS AND PROPRIETARY RIGHTS
 
Our success will depend in part on our ability to obtain United States and
foreign patent protection for our drug candidates and processes, preserve our
trade secrets and operate without infringing the proprietary rights of third
parties. We place considerable importance on obtaining patent protection for
significant new technologies, products and processes. Legal standards relating
to the validity of patents covering pharmaceutical and biotechno-
 
                                        4
<PAGE>   6
 
logical inventions and the scope of claims made under such patents are still
developing. Our patent position is highly uncertain and involves complex legal
and factual questions. We cannot be certain that the applicant or inventors of
subject matter covered by patent applications or patents owned by or licensed to
us were the first to invent or the first to file patent applications for such
inventions. We cannot guarantee that any patents will issue from any of the
pending or future patent applications we own or have licensed. Existing or
future patents owned by or licensed to us may be challenged, infringed upon,
invalidated, found to be unenforceable or circumvented by others. Further, we
cannot guarantee that any rights we may have under any issued patents will
provide us with sufficient protection against competitive products or otherwise
cover commercially valuable products or processes.
 
If another party claims the same subject matter or subject matter overlapping
with the subject matter that we have claimed in a United States patent
application or patent, we may decide or be required to participate in
interference proceedings in the United States Patent and Trademark Office in
order to determine the priority of invention. Loss of such an interference
proceeding would deprive us of patent protection sought or previously obtained.
Participation in such proceedings could result in substantial costs, whether or
not the eventual outcome is favorable.
 
GOVERNMENT REGULATION AND PRODUCT APPROVALS
 
Our drug candidates under development are subject to regulation by the federal
government, including the FDA, and by state and local governments. If our
products are marketed abroad, they will also need to comply with export
requirements and regulation by foreign governments. The applicable regulatory
approval process is lengthy and expensive and must be completed prior to the
commercialization of a product. We cannot guarantee that we will be able to
obtain necessary regulatory approvals on a timely basis, if at all, for any of
our products under development. Delays in receiving such approvals, failure to
receive such approvals at all or failure to comply with existing or future
regulatory requirements could have a material adverse effect on our business,
financial condition and results of operations.
 
Product development and approval to meet FDA regulatory requirements takes a
number of years, involves the expenditure of substantial resources and is
uncertain. Many products that initially appear promising ultimately do not reach
the market because they are not found to be safe or effective. In addition, the
current regulatory framework could change and additional regulations may arise
at any stage of product development that may affect approval, delay the
submission or review of an application or require additional expenditures.
 
SUBSTANTIAL CAPITAL NEEDS
 
We will require substantial additional funds in order to finance our drug
discovery and development programs, fund operating expenses, pursue regulatory
clearances, develop manufacturing, marketing and sales capabilities, and
prosecute and defend our intellectual property rights. We intend to seek
additional funding through public or private financing or through collaboration
arrangements with collaborative partners. If we raise funds by selling equity
securities, sales may dilute your share ownership and future investors may be
granted rights superior to yours. We cannot guarantee, however, that we will be
able to obtain additional financing on acceptable terms, if at all.
 
                                        5
<PAGE>   7
 
TECHNOLOGICAL CHANGE AND COMPETITION
 
Biotechnology and related pharmaceutical technology have undergone rapid and
significant change. We expect that the technologies associated with
biotechnology research and development will continue to develop rapidly. Our
future will depend in large part on our ability to maintain a competitive
position with respect to these technologies. Any compounds, products or
processes that we develop may become obsolete before we recover any expenses we
have incurred in connection with developing these products.
 
The biotechnology and pharmaceutical industries are intensely competitive. We
have numerous competitors in the United States and elsewhere. Our competitors
include major, multinational pharmaceutical and chemical companies, specialized
biotechnology firms and universities and other research institutions. Many of
these competitors have greater financial and other resources, larger research
and development staffs and more effective marketing and manufacturing
organizations than we do. In addition, academic and government institutions have
become increasingly aware of the commercial value of their research findings.
These institutions are now more likely to enter into exclusive licensing
agreements with commercial enterprises, including our competitors, to market
commercial products.
 
Our competitors may succeed in developing or licensing technologies and drugs
that are more effective or less costly than any we are developing. Our
competitors may succeed in obtaining FDA or other regulatory approvals for drug
candidates before we do. We cannot guarantee that our drug candidates, if
approved for sale, will be able to compete successfully with our competitors'
existing products under development.
 
NO SALES AND MARKETING EXPERIENCE
 
Our efforts to date have focused on the development and evaluation of our drug
candidates. As we continue clinical studies and prepare for commercialization of
our drug candidates, we need to build a sales and marketing infrastructure. We
have no experience in the sales and marketing of our drug candidates. We may not
be able to attract and retain the skilled personnel necessary to effectively
market our drug candidates.
 
DEPENDENCE ON LICENSE AGREEMENTS
 
We license our drug candidates from Dr. Patrick T. Prendergast and from
Edenland, Inc. and Colthurst Limited, two organizations Dr. Prendergast
controls. Our license agreements can be terminated if we materially breach our
obligations under the agreements. Termination of our license agreements would
cause us to lose our rights to our existing drug candidates. If we lost our
licensed rights to one or more of our drug candidates or if our rights were
materially limited, it would have a material adverse effect on our business,
operating results and financial condition.
 
DEPENDENCE ON OFFICERS AND FUTURE EMPLOYEES
 
Our ability to successfully implement our business strategy depends highly upon
our Chief Executive Officer, Richard B. Hollis. The loss of Mr. Hollis's
services could impede the achievement of our research and development
objectives. We also highly depend on our ability to hire and retain qualified
scientific and technical personnel. The competition for these employees is
intense. We cannot guarantee that we will continue to be able to hire and retain
the qualified personnel needed for our business. Loss of the services of or the
 
                                        6
<PAGE>   8
 
failure to recruit key scientific and technical personnel could adversely affect
our business, operating results and financial condition.
 
TECHNOLOGICAL UNCERTAINTIES
 
Our product development efforts are based upon technologies and therapeutic
approaches that have not been widely used in humans for therapeutic purposes.
There is significant risk that these approaches will not prove to be successful.
Although we believe that the positive results obtained to date in preclinical
and limited clinical human studies support further research and development, the
positive results obtained to date do not necessarily reflect results that we may
obtain in further human clinical testing.
 
PHARMACEUTICAL PRICING AND PENDING HEALTH CARE REFORMS
 
Government health administration authorities, together with private health
insurers, increasingly are attempting to contain health care costs by limiting
the price or reimbursement levels for medical products and services. In certain
foreign markets, pricing or profitability of prescriptive pharmaceuticals is
subject to government control. In the United States, there have been a number of
federal and state proposals to implement similar government controls or
otherwise significantly reform the existing health care system. We cannot
predict if any of these reform proposals will be adopted, when they may be
adopted, or what impact they may have on Hollis-Eden. Any enacted legislation
may include provisions resulting in price limits, utilization controls or other
consequences that may adversely affect our business, operating results and
financial condition.
 
MANUFACTURING LIMITATIONS AND UNCERTAINTIES
 
Outside manufacturers currently produce our drug candidates and supply us with
sufficient quantities to conduct clinical trials. If we have difficulty in the
future obtaining our required quantity or quality of supply, we could experience
significant delays in our development programs or regulatory approval process.
If we have difficulties establishing relationships with manufacturers to produce
and distribute our finished pharmaceutical products, market introduction and
sales of our products would be adversely affected. Manufacturers producing our
products must also follow current Good Manufacturing Practices regulations
enforced by the FDA through its facilities inspection program. We may not be
able to commercialize pharmaceutical products as planned if we cannot obtain or
retain qualified third party manufacturing on commercially acceptable terms.
 
We currently do not intend to manufacture any pharmaceutical products ourselves.
If we determine to manufacture products ourselves in the future, we would be
subject to the regulatory requirements described above and would be subject to
the same risks regarding difficulties encountered in manufacturing
pharmaceutical products. We also would require substantial additional capital.
We have no experience manufacturing pharmaceutical products for commercial
purposes, so we cannot guarantee that we would be able to manufacture any
products successfully or in a cost-effective manner.
 
MANAGEMENT OF GROWTH
 
We will need to continue to improve and expand our management, operational and
financial systems and controls to support future growth. Our business, operating
results and financial condition will be adversely affected if we cannot do so.
 
                                        7
<PAGE>   9
 
PRODUCT LIABILITY AND LACK OF ADEQUATE INSURANCE
 
Our business exposes us to potential product liability risks associated with the
testing, manufacturing, marketing and sale of pharmaceutical products.
Therefore, product liability claims may be asserted against us. Product
liability insurance for the pharmaceutical industry generally is expensive, if
it is available at all. Adequate insurance coverage may not be available at an
acceptable cost. A product liability claim could adversely affect our business,
operating results and financial condition.
 
YEAR 2000
 
Many currently installed computer systems and software products are coded to
accept only two-digit entries in the date code field. Beginning in the year
2000, these date code fields will need to accept four-digit entries to
distinguish the 21st century dates from 20th century dates. As a result, in less
that two years, computer systems and software used by many companies may need to
be upgraded to comply with Year 2000 requirements.
 
We upgraded our accounting software this quarter to make it Year 2000 compliant.
We also upgraded some of our computer operating systems and the remainder is
scheduled for upgrading before the end of this year. Once the upgrades are
completed, we believe our computer systems and applications will be Year 2000
compliant.
 
We have recently begun reviewing our communications systems and other
non-information technology systems to ascertain whether they are Year 2000
compliant. We expect to complete our review by December 1998.
 
We do not expect that the costs associated with achieving Year 2000 compliance
will have a material adverse effect on our future results of operations,
liquidity or capital resources. We have spent less than one thousand dollars in
connection with our Year 2000 compliance efforts to date. We believe that the
costs to review our non-information technology systems will be immaterial.
 
We have begun contacting our material suppliers and third party service
providers to identify their Year 2000 problems and provide solutions to prevent
the disruption of our business activities. Currently we have very little
information regarding the extent of Year 2000 compliance by our suppliers and
third party service providers. We expect to complete our review of these
parties' compliance efforts in March 1999.
 
We cannot guarantee that the computer systems and applications of other
companies which we rely upon will be timely converted. Any such failure by these
other companies to become Year 2000 compliant could materially adversely affect
us. Moreover, the following could have a material adverse effect on our business
or financial condition:
 
     - failure of suppliers and third-party service providers' equipment to
       operate accurately;
 
     - failure of clinical trial site medical equipment to perform properly;
 
     - failure of necessary materials or supplies to be available to us when
       needed; or
 
     - failure of other equipment, software, or systems as a result of 2000
       problems.
 
We intend to assess worst case scenarios and to develop one or more contingency
plans that may be necessary, such as securing alternative vendors, at the
completion of our review of our material suppliers and third-party service
providers.
 
                                        8
<PAGE>   10
 
AUTHORIZED PREFERRED STOCK
 
Holders of our preferred stock have certain rights that are not held by holders
of our common stock. In addition, our Board of Directors is authorized, without
any further vote by the stockholders, to issue additional shares of preferred
stock and to designate the rights, preferences and privileges of such preferred
stock, including voting, dividend and liquidation rights. The rights of any
preferred stock issued by Hollis-Eden in the future may be superior to those of
the holders of common stock. Therefore, the issuance of additional preferred
stock could materially adversely affect the rights of holders of common stock.
 
INDEMNIFICATION AND LIMITED MONETARY DAMAGES
 
Our Certificate of Incorporation provides that our directors will not be liable
for monetary damages to our stockholders except as required by law. In addition,
our Bylaws indemnify our officers and directors to the fullest extent permitted
by Delaware law. Therefore, our stockholders' rights are limited in comparison
to the rights of stockholders of a corporation that has not adopted such
provisions because our stockholders may not be able to prevail in actions for
monetary damages against our directors. In addition, we may incur substantial
financial losses to the extent that we indemnify our officers and directors.
 
DIVIDENDS UNLIKELY
 
We have never declared or paid dividends on our stock. We do not intend to
declare or pay any dividends in the foreseeable future.
 
CONCENTRATION OF OWNERSHIP
 
Richard B. Hollis, our Chief Executive Officer, owns approximately 33% of our
outstanding common stock (assuming no exercise of outstanding warrants or
options and no conversion of Preferred Stock). Accordingly, Mr. Hollis can
effectively control our business, policies and affairs, including the election
of members of our Board of Directors. Assuming the exercise of our outstanding
warrants and options and the conversion of Preferred Stock (at an estimated
conversion price of $20.00), Mr. Hollis would own approximately 21% of our
outstanding common stock, and Mr. Terren S. Peizer, our President and one of our
Directors, would own approximately 15% of the outstanding common stock.
 
CLASSIFIED BOARD OF DIRECTORS
 
Our Board of Directors is a "classified board," with approximately one-third of
our directors elected each year. Two annual meetings would be necessary to
change a majority of the directors as a result of having a classified board. The
existence of a classified board may, in certain circumstances, deter or delay
mergers, tender offers, other possible takeover attempts or changes in
management of the Board of Directors which may be favored by some or a majority
of our stockholders.
 
VOLATILITY OF STOCK MARKET COULD DRIVE DOWN PRICE OF OUR COMMON STOCK
 
The market prices for securities of life sciences companies, particularly those
that are not profitable, have been highly volatile, especially recently.
Publicized events and announcements may have a significant impact on the market
price of our common stock. For example, biological or medical discoveries by
competitors, unfavorable results from clinical
 
                                        9
<PAGE>   11
 
trials, unfavorable developments concerning patents or other proprietary rights
or unfavorable domestic or foreign regulatory developments may have the effect
of temporarily or permanently driving down the price of our common stock. In
addition, the stock market from time to time experiences extreme price and
volume fluctuations which particularly affect the market prices for emerging and
life sciences companies, such as ours, and which are often unrelated to the
operating performance of the affected companies. These broad market fluctuations
may adversely affect the ability of a stockholder to dispose of his shares at a
price equal to or above the price at which the shares were purchased.
 
                                       10
<PAGE>   12
 
                              SELLING STOCKHOLDERS
 
The following table sets forth the names of the selling stockholders, and the
number of shares of common stock owned beneficially by them as of December 15,
1998 which may be offered pursuant to this prospectus. This information is based
upon information provided by each selling stockholder. Because the selling
stockholders may offer all, some or none of their respective shares of common
stock, no definitive estimate as to the number of shares thereof that will be
held by the selling stockholders after such offering can be provided. The term
"selling stockholder" includes the stockholders listed below and their
transferees, pledgees, donees or other successors.
 
<TABLE>
<CAPTION>
NAME                                                        SHARES BEING OFFERED(1)
<S>                                                         <C>
James D. Bowyer...........................................          158,491
Christopher A. Marlett....................................          142,641
LHIP Acquisition Company..................................          135,849
Dyana Marlett.............................................           15,849
International Investor Relations Group....................            3,493
Boniface Costa............................................           22,222
Growth Ventures, Inc. Pension Plan and Trust..............          189,938
Inverness Investments Profit Sharing Plan.................           99,999
Leonard Rothstein.........................................           49,999
Jodi Rothstein............................................           50,000
B.A. Bates................................................           20,964
Underwood Family Partners.................................           20,964
Brenman, Key & Bromberg, P.C..............................           20,964
                                                                    -------
          Total...........................................          931,373
                                                                    =======
</TABLE>
 
- -------------------------
(1) Includes 927,880 shares of common stock issuable upon the exercise of
    certain warrants.
 
None of the selling stockholders has, or within the past three years has had,
any position, office or other material relationship with Hollis-Eden or any of
its predecessors or affiliates.
 
                              PLAN OF DISTRIBUTION
 
The shares of common stock may be sold from time to time by the selling
stockholders in one or more transactions at fixed prices, at market prices at
the time of sale, at varying prices determined at the time of sale or at
negotiated prices. The selling stockholders may offer their shares of common
stock in one or more of the following transactions:
 
     - on any national securities exchange or quotation service at which the
       common stock may be listed or quoted at the time of sale, including the
       Nasdaq National Market.
 
     - in the over-the-counter market,
 
     - in private transactions,
 
     - through options,
 
     - by pledge to secure debts and other obligations, or a combination of any
       of the above transactions.
 
                                       11
<PAGE>   13
 
If required, we will distribute a supplement to this prospectus to describe
material changes in the terms of the offering.
 
The shares of common stock described in this prospectus may be sold from time to
time directly by the selling stockholders. Alternatively, the selling
stockholders may from time to time offer shares of common stock to or through
underwriters, broker/dealers or agents. The selling stockholders and any
underwriters, broker/dealers or agents that participate in the distribution of
the shares of common stock may be deemed to be "underwriters" within the meaning
of the Securities Act of 1933. Any profits on the resale of shares of common
stock and any compensation received by any underwriter, broker/dealer or agent
may be deemed to be underwriting discounts and commissions under the Securities
Act of 1933.
 
Any shares covered by this prospectus which qualify for sale pursuant to Rule
144 under the Securities Act of 1933 may be sold under rule 144 rather than
pursuant to this prospectus. The selling stockholders may not sell all of the
shares. The selling stockholders may transfer, devise or gift such shares by
other means not described in this prospectus.
 
To comply with the securities laws of certain jurisdictions, the common stock
must be offered or sold only through registered or licensed brokers or dealers.
In addition, in certain jurisdictions, the common stock may not be offered or
sold unless they have been registered or qualified for sale or an exemption is
available and complied with.
 
Under the Securities Exchange Act of 1934, any person engaged in a distribution
of the common stock may not simultaneously engage in market-making activities
with respect to the common stock for nine business days prior to the start of
the distribution. In addition, each selling stockholder and any other person
participating in a distribution will be subject to the Securities Exchange Act
of 1934 which may limit the timing of purchases and sales of common stock by the
selling stockholders or any such other person. These factors may affect the
marketability of the common stock and the ability of brokers or dealers to
engage in market-making activities.
 
All expenses of this registration will be paid by Hollis-Eden. These expenses
include the SEC's filing fees and fees under state securities or "blue sky"
laws. We estimate that our expenses in connection with this offering will be
approximately $11,000. All expenses for the issuance of a supplement to this
prospectus, when requested by selling stockholder(s), will be paid by the
requesting stockholder(s).
 
                                 LEGAL MATTERS
 
Cooley Godward LLP will give its opinion that the shares offered in this
prospectus have been validly issued and are fully paid and non-assessable, and
that the shares which will be issued upon the exercise of certain warrants will
be validly issued, fully paid and nonassessable.
 
                                    EXPERTS
 
The financial statements of the registrant as of December 31, 1997 and 1996 and
for each of the years ended December 31, 1997, 1996 and 1995 and for the period
August 15, 1994 (inception) to December 31, 1997 have been audited by BDO
Seidman, LLP, as set forth in its report thereon included in Hollis-Eden's
Annual Report on Form 10-K for the year ended December 31, 1997 and incorporated
herein by reference. Such financial statements are incorporated herein by
reference in reliance upon such reports given upon the authority of said firm as
experts in accounting and auditing.
 
                                       12
<PAGE>   14
 
===============================================================================
 
WE HAVE NOT AUTHORIZED ANY DEALER, SALESPERSON OR OTHER PERSON TO GIVE ANY
INFORMATION OR TO MAKE ANY REPRESENTATIONS NOT CONTAINED IN THIS PROSPECTUS OR
ANY PROSPECTUS SUPPLEMENT. YOU MUST NOT RELY ON ANY UNAUTHORIZED INFORMATION.
THIS PROSPECTUS IS NOT AN OFFER OF THESE SECURITIES IN ANY STATE WHERE AN OFFER
IS NOT PERMITTED. THE INFORMATION IN THIS PROSPECTUS IS CURRENT AS OF DECEMBER
24, 1998. YOU SHOULD NOT ASSUME THAT THIS PROSPECTUS IS ACCURATE AS OF ANY OTHER
DATE.
 
          -------------------------
                      
              TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                       PAGE
                                       ----
<S>                                    <C>
Where You Can Get More Information...   2.
The Company..........................   3.
Use of Proceeds......................   3.
Risk Factors.........................   4.
Selling Stockholders.................  11.
Plan of Distribution.................  11.
Legal Matters........................  12.
Experts..............................  12.
</TABLE>
 
===============================================================================





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



                                 931,373 Shares
                                        
                                        
                                  HOLLIS-EDEN
                                PHARMACEUTICALS,
                                      INC.
                                        
                                        
                                  Common Stock



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


<PAGE>   15
 
                                    PART II
 
                     INFORMATION NOT REQUIRED IN PROSPECTUS
 
ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.
 
The expenses in connection with the issuance and distribution of the securities
being registered are set forth in the following table (all amounts except the
registration fee and the listing fee are estimated):
 
<TABLE>
<S>                                                          <C>
SEC Registration Fee.......................................  $ 4,013.00
Legal fees and expenses....................................  $ 5,000.00
Accounting fees and expenses...............................  $ 3,000.00
                                                             ----------
          Total............................................  $12,013.00
                                                             ==========
</TABLE>
 
ITEM 15. INDEMNIFICATION OF OFFICERS AND DIRECTORS.
 
Under Section 145 of the Delaware General Corporation Law, the registrant has
broad powers to indemnify its directors and officers against liabilities they
may incur in such capacities, including liabilities under the Securities Act of
1933, as amended (the "Securities Act").
 
The registrant's bylaws provide that the registrant shall indemnify its
directors and executive officers and may indemnify its other officers, employees
and other agents to the fullest extent permitted by Delaware law. The registrant
is also empowered under its bylaws to enter into indemnification contracts with
its directors and officers and to purchase insurance on behalf of any person
whom it is required or permitted to indemnify. In addition, the registrant is
required, subject to certain exceptions, to advance all expenses incurred by any
director or executive officer in connection with a completed, pending or
threatened action, suit or proceeding upon receipt of an undertaking by such
director or executive officer to repay all amounts advanced by the registrant on
such person's behalf if it is ultimately determined that such person is not
entitled to be indemnified under the bylaws or otherwise.
 
The registrant's Certificate of Incorporation provides that to the fullest
extent permitted under Delaware law, the registrant's directors will not be
personally liable to the registrant and its stockholders for monetary damages
for any breach of a director's fiduciary duty. The Certificate of Incorporation
does not, however, eliminate the duty of care, and in appropriate circumstances,
equitable remedies such as an injunction or other forms of non-monetary relief
would remain available under Delaware law. Each director is subject to liability
for breach of the director's duty of loyalty to the registrant, for acts or
omissions not in good faith or involving intentional misconduct or knowing
violations of law, for any transaction from which the director derived an
improper personal benefit and for improper distributions to stockholders and
loans to directors and officers. This provision does not affect a director's
responsibilities under any other laws, such as the federal securities laws or
state or federal environmental laws.
 
The registrant maintains directors' and officers' liability insurance.
 
                                      II-1
<PAGE>   16
 
ITEM 16. EXHIBITS.
 
(a) Exhibits.
 
<TABLE>
<CAPTION>
    EXHIBIT NO.                           DESCRIPTION
    -----------                           -----------
    <S>           <C>
    5.1           Opinion of Cooley Godward LLP.
    23.1          Consent of BDO Seidman, LLP.
    23.2          Consent of Cooley Godward LLP. Reference is made to Exhibit
                  5.1.
    24.1          Power of Attorney. Reference is made to page II-4.
</TABLE>
 
ITEM 17. UNDERTAKINGS.
 
Insofar as indemnification for liabilities arising under the Securities Act may
be permitted to directors, officers or persons controlling the registrant
pursuant to the provisions described in Item 15, the registrant has been
informed that in the opinion of the Securities and Exchange Commission, such
indemnification is against public policy as expressed in the Securities Act and
is 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 person controlling the registrant in
the successful defense of any action, suit or proceeding) is asserted by such
director, officer or person controlling the registrant in connection with the
securities being registered, the registrant will, unless in the opinion of its
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 of 1933 and will be
governed by the final adjudication of such issue.
 
The undersigned registrant hereby undertakes:
 
     (1) To file, during any period in which offers or sales are being made
     pursuant to this registration statement, a post-effective amendment to this
     registration statement 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;
 
     (2) That, for the purpose of determining any liability under the Securities
     Act of 1933, each such post-effective amendment shall be deemed to be a new
     registration statement relating to the securities offered therein, and the
     offering of such securities at that time shall be deemed to be the initial
     bona fide offering thereof; and
 
     (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 undertakes that, for purposes of determining any
liability under the Securities Act of 1933, each filing of the registrant's
annual report pursuant to Section 13(a) or 15(d) of the Securities Exchange Act
of 1934 (and, where applicable, each filing of an employee benefit plan's annual
report pursuant to Section 15(d) of the Securities Exchange Act of 1934) that is
incorporated by reference in the registration statement shall be deemed to be a
new registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial bona
fide offering thereof.
 
                                      II-2
<PAGE>   17
 
                                   SIGNATURES
 
Pursuant to the requirements of the Securities Act of 1933, the registrant
certifies that it has reasonable grounds to believe that it 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 San Diego, State of California, on December 23, 1998.
 
                                     HOLLIS-EDEN PHARMACEUTICALS, INC.
 
                                     By:        /s/ RICHARD B. HOLLIS
                                        --------------------------------------
                                                   Richard B. Hollis
                                               Chairman of the Board and
                                                Chief Executive Officer
 
                                      II-3
<PAGE>   18
 
                               POWER OF ATTORNEY
 
KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears
below constitutes and appoints Richard B. Hollis, Terren S. Peizer and Robert W.
Weber and each of them, his true and lawful attorney-in-fact and agent, with
full power of substitution and resubstitution, for him and in his 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, and each of them, full power and authority to do and perform each and
every act and thing requisite and necessary to be done in connection therewith,
as fully to all intents and purposes as he might or could do in person, hereby
ratifying and confirming all that said attorney-in-fact and agent, or any of
them, or his substitutes or substitute, 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>
                   SIGNATURE                              TITLE                DATE
                   ---------                              -----                ----
<S>                                               <C>                    <C>
/s/ RICHARD B. HOLLIS                             Chairman of the        December 23, 1998
- ------------------------------------------------  Board, Chief
Richard B. Hollis                                 Executive Officer and
                                                  Director (Principal
                                                  Executive Officer)
 
/s/ TERREN S. PEIZER                              President and          December 23, 1998
- ------------------------------------------------  Director
Terren S. Peizer
 
/s/ ROBERT W. WEBER                               Vice President-        December 23, 1998
- ------------------------------------------------  Controller (Principal
Robert W. Weber                                   Financial and
                                                  Accounting Officer)
 
/s/ THOMAS CHARLES MERIGAN, JR.                   Chairman of the        December 23, 1998
- ------------------------------------------------  Scientific Advisory
Thomas Charles Merigan, Jr.                       Board and Director
 
                                                  Director               December 23, 1998
- ------------------------------------------------
J. Paul Bagley III
 
                                                  Director               December 23, 1998
- ------------------------------------------------
Salvatore J. Zizza
 
                                                  Director               December 23, 1998
- ------------------------------------------------
Brendan R. McDonnell
 
/s/ LEONARD MAKOWKA                               Director               December 23, 1998
- ------------------------------------------------
Leonard Makowka
</TABLE>
 
                                      II-4
<PAGE>   19
 
                                 EXHIBIT INDEX
 
<TABLE>
<CAPTION>
EXHIBIT NO.                            DESCRIPTION
- -----------                            -----------
<C>            <S>
    5.1        Opinion of Cooley Godward LLP.
   23.1        Consent of BDO Seidman, LLP.
   23.2        Consent of Cooley Godward LLP. Reference is made to Exhibit
               5.1.
   24.1        Power of Attorney. Reference is made to Page II-4.
</TABLE>

<PAGE>   1
                                                                     EXHIBIT 5.1


                        [COOLEY GODWARD LLP LETTERHEAD]



December 23, 1998

HOLLIS-EDEN PHARMACEUTICALS, INC.
9333 Genesee Avenue, Suite 110
San Diego, CA  92121


Ladies and Gentlemen:

You have requested our opinion with respect to certain matters in connection
with the filing by HOLLIS-EDEN PHARMACEUTICALS, INC. (the "Company") of a Form
S-3 Registration Statement (the "Registration Statement"), including a related
prospectus filed with the Registration Statement (the "Prospectus"), covering
the registration of an aggregate of 931,373 shares of the Company's Common
Stock, $.01 par value, that may be sold by certain selling stockholders,
including 927,880 shares of Common Stock (the "Warrant Shares") issuable upon
the exercise of certain warrants (the "Warrants") and 3,493 shares of Common
Stock (the "Shares").

In connection with this opinion, we have examined the Registration Statement and
related Prospectus, your Certificate of Incorporation and Bylaws, as amended,
the Warrants and related agreements, and such other documents, records,
certificates, memoranda and other instruments as we deem necessary as a basis
for this opinion. We have assumed the genuineness and authenticity of all
documents submitted to us as originals, the conformity to originals of all
documents submitted to us as copies thereof and the due execution and delivery
of all documents where due execution and delivery are a prerequisite to the
effectiveness thereof.

On the basis of the foregoing, and in reliance thereon, we are of the opinion
(i) that the Shares are validly issued, fully paid and nonassessable, and (ii)
that the Warrant Shares, when issued and sold in accordance with the terms of
the Warrants, will be validly issued, fully paid and nonassessable.

We consent to the reference to our firm under the caption "Legal Matters" in the
Prospectus included in the Registration Statement and to the filing of this
opinion as an exhibit to the Registration Statement.

Very truly yours,

Cooley Godward LLP



Jeremy D. Glaser

<PAGE>   1
 
                                                                    EXHIBIT 23.1
 
              CONSENT OF INDEPENDENT CERTIFIED PUBLIC ACCOUNTANTS
 
Hollis-Eden Pharmaceuticals, Inc.
San Diego, California
 
We hereby consent to the incorporation by reference in the Prospectus
constituting a part of the Registration Statement on Form S-3 of our report
dated March 6, 1998, relating to the financial statements of Hollis-Eden
Pharmaceuticals, Inc. appearing in the Company's Annual Report on Form 10-K for
the year ended December 31, 1997.
 
We also consent to the reference to us under the caption "Experts" in the
Prospectus.
 
                                          BDO SEIDMAN, LLP
 
New York, New York
December 23, 1998



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