HOLLIS EDEN PHARMACEUTICALS INC /DE/
S-3, 2000-12-05
PHARMACEUTICAL PREPARATIONS
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<PAGE>

   As filed with the Securities and Exchange Commission on December 5, 2000
                                                     Registration No. 333-
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                      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                         (I.R.S. Employer
        of incorporation or organization)                    Identification Number)
</TABLE>

                        9333 Genesee Avenue, Suite 200
                          San Diego, California 92121
                                (858) 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 200
                          San Diego, California 92121
                                (858) 587-9333
(Name, address, including zip code, and telephone number, including area code,
                             of agent for service)

                               ---------------
                                  Copies to:
                             Eric J. Loumeau, Esq.
                       HOLLIS-EDEN PHARMACEUTICALS, INC.
                        9333 Genesee Avenue, Suite 200
                          San Diego, California 92121
                                (858) 587-9333

                               ---------------
  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. [_]

                        CALCULATION OF REGISTRATION FEE
<TABLE>
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<CAPTION>
                                          Proposed        Proposed
 Title of each class of                   maximum          maximum       Amount of
    securities to be       Amount to   offering price     aggregate     registration
       registered        be registered  per share(1)  offering price(1)     fee
------------------------------------------------------------------------------------
<S>                      <C>           <C>            <C>               <C>
Common Stock, $.01 par
 value.................     228,672        $4.25          $971,856        $256.57
------------------------------------------------------------------------------------
</TABLE>
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(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
    November 29, 2000 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.
-------------------------------------------------------------------------------
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<PAGE>

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+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.                                                        +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

                 SUBJECT TO COMPLETION, DATED DECEMBER 5, 2000

PROSPECTUS

                                 228,672 Shares

                       HOLLIS-EDEN PHARMACEUTICALS, INC.

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

                                  Common Stock

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

  Selling stockholders identified in this prospectus are selling 228,672 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 1, 2000, was $5.81per share.

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

         Investing in the common stock involves a high degree of risk.

                    See "Risk Factors," beginning on page 3.

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

  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           , 2000.
<PAGE>

                               TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                                                            Page
                                                                            ----
       <S>                                                                  <C>
       Hollis-Eden Pharmaceuticals.........................................   3

       Use of Proceeds.....................................................   3

       Risk Factors........................................................   3

       Where You Can Get More Information..................................   7

       Forward-Looking Statements..........................................   7

       Selling Stockholders................................................   8

       Plan of Distribution................................................   9

       Legal Matters.......................................................  10

       Experts.............................................................  10
</TABLE>

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

  This prospectus is part of a registration statement we filed with the
Securities and Exchange Commission. You should rely only on the information
contained in or incorporated by reference in this prospectus. 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 considered to be
part of this prospectus, and information that we file later with the SEC will
automatically update and supersede this information.

                                       2
<PAGE>

                          HOLLIS-EDEN PHARMACEUTICALS

  Hollis-Eden is a pharmaceutical company in the development stage. We intend
to discover, develop and commercialize products for the treatment of a wide
array of infectious diseases and immune system disorders including HIV/AIDS,
hepatitis, and malaria.

  Hollis-Eden's executive offices are located at 9333 Genesee Avenue, Suite
200, San Diego, California 92121, telephone number (858) 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.

                                 RISK FACTORS

  An investment in Hollis-Eden shares involves a high degree of risk. You
should consider the following discussion of risks, in addition to other
information contained in this prospectus. This prospectus also contains
forward-looking statements that involve risks and uncertainties.

If we do not obtain FDA regulatory approval for our products, we cannot sell
our products and we will not generate revenues.

  Our principal development efforts are currently centered around HE2000, a
drug candidate which we believe shows promise for the treatment of a variety
of infectious diseases and immune system disorders. However, all drug
candidates 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. We expect to
incur significant additional operating losses over the next several years as
we fund development, clinical testing and other expenses while seeking
regulatory approval. 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 cannot guarantee that any of our product candidates will obtain required
government approval. If we do not receive FDA or foreign approvals for our
products, we will not be able to sell our products and will not generate
revenues.

If we do not successfully commercialize our products, we may never achieve
profitability.

  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 and have never
commercially introduced a product. Our accumulated deficit was $49.8 million
through September 30, 2000. 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. If we are unable to
develop safe, commercially viable drugs, we may never achieve profitability.

As a result of our intensely competitive industry, we may not gain enough
market share to be profitable.

  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

                                       3
<PAGE>

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. If we are unable to compete successfully,
we may never be able to sell enough products at a sufficient price that would
generate profits.

Our failure to protect our proprietary technology could impair our competitive
position.

  We have developed and licensed numerous issued patents and pending
applications in the U.S. and foreign counterparts. Our success will depend in
part on our ability to obtain additional 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 biotechnology 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
and could prevent us from commercializing our products. Participation in such
proceedings could result in substantial costs, whether or not the eventual
outcome is favorable. These additional costs could adversely affect our
ability to achieve profitability.

We will need to raise additional money before we expect to achieve
profitability; if we fail to raise additional money, it would be difficult to
continue our business.

  As of September 30, 2000 our cash and cash equivalents totaled approximately
$39 million. We believe these financial resources will fund our opportunities
well into 2002. Once these current financial resources run out, 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 cannot raise
additional funds when needed, we may not be able to continue to develop our
products, which would prevent us from generating revenues.

If we raise additional money by issuing equity securities, your investment
will be diluted.

  If we raise additional funding by issuing more equity securities, the new
shares will dilute the voting power of your investment on a percentage basis.

                                       4
<PAGE>

The technology in our sector is developing rapidly, and our future depends on
our ability to keep abreast of technological change.

  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. If we fail to
recover our expenses because our products become obsolete, we may not be able
to achieve profitability.

If the manufacturers of our products do not comply with FDA regulations, or
cannot produce the amount of products we need to continue our development, we
will fall behind on our business objectives.

  Outside manufacturers currently produce our drug candidates. Manufacturers
producing our products must follow current Good Manufacturing Practices
regulations enforced by the FDA through its facilities inspection program. If
a manufacturer of our products does not conform to the Good Manufacturing
Practices regulations and cannot be brought up to such a standard, we will be
required to find alternative manufacturers that do conform. This may be a long
and difficult process, and may delay our ability to receive FDA approval of
our products.

  We also rely on our manufacturers to supply us with a sufficient quantity of
our drug candidates to conduct clinical trials. If we have difficulty in the
future obtaining our required quantity and quality of supply, we could
experience significant delays in our development programs and regulatory
process.

If we decide to manufacture our products ourselves, we face further FDA
regulation and will require additional capital.

  At this time, we do not intend to manufacture any pharmaceutical products
ourselves. If we decide to manufacture products ourselves in the future, we
would be subject to the same risks associated with the regulatory requirements
described above. We would also 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.

Our ability to achieve any significant revenue will depend on our ability to
establish effective sales and marketing capabilities.

  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. If we fail to establish a sufficient marketing and sales
force, it will impair our ability to enter new or existing markets. Our
inability to effectively enter these markets would materially and adversely
affect our ability to generate significant revenues.

If Hollis-Eden were to lose the services of Richard B. Hollis, or fail to
attract qualified personnel in the future, our business objectives would be
more difficult to implement, adversely affecting our operations.

  Our ability to successfully implement our business strategy depends highly
upon our Chief Executive Officer, Richard B. Hollis. The loss of Mr. Hollis'
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 failure to recruit key scientific and technical personnel could
adversely affect our business, operating results and financial condition.


                                       5
<PAGE>

We may face product liability claims related to the use or misuse of our
products which may cause us to incur significant losses.

  We face inherent business risk of product liability claims in the event that
the use or misuse of our products results in personal injury or death. We have
not experienced any such claims to date, but we cannot be certain, in
particular after commercial introduction of our products, that we will not
experience losses due to product liability claims. We currently maintain
liability insurance on a claims-made basis. We cannot be certain that the
insurance policies' coverage limits are adequate. The insurance is expensive,
difficult to obtain and may not be available in the future on acceptable
terms, or at all. Any claims against us, regardless of their merit, could
substantially increase our costs and cause us to incur significant losses.

Trading in our shares could be subject to extreme price fluctuations that
could adversely affect your investment.

  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 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
(example: Hollis-Eden's stock price has ranged from $4.00 to $19.25 from
January 1, 2000 to December 1, 2000.) 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.

Because stock ownership is concentrated, you and other investors will have
minimal influence on stockholders decisions.

  Assuming that outstanding warrants and options have not been exercised,
Richard B. Hollis, our Chief Executive Officer, owns approximately 24% of our
outstanding common stock. Assuming the exercise of our outstanding warrants
and options, Mr. Hollis would own approximately 20% of our outstanding common
stock. As a result, Mr. Hollis may be able to significantly influence the
management of Hollis-Eden and all matters requiring stockholder approval,
including the election of directors. Such concentration of ownership may also
have the effect of delaying or preventing a change in control of Hollis-Eden.

We have implemented anti-takeover provisions, any of which may reduce the
market price of our common stock.

  Provisions of our certificate of incorporation and bylaws could make it more
difficult for a third party to acquire us, even if the acquisition would be
beneficial to our stockholders.

  Our board of directors is authorized, without any further vote by
stockholders, to issue shares of preferred stock. The issuance of preferred
stock with special voting, liquidation and dividend privileges may have the
effect of delaying, deferring or preventing a change in control without any
further action by the stockholders. Any such issuance may materially and
adversely affect the price of the common stock.

  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.

  We have distributed a dividend of one right for each outstanding share of
common stock pursuant to the terms of our stockholder rights plan. These
rights will cause substantial dilution to the ownership of a person or

                                       6
<PAGE>

group that attempts to acquire us on terms not approved by our board of
directors and may have the effect of deterring hostile takeover attempts.

                      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".

  We incorporate by reference the documents listed below, except as modified
by this registration statement, 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, 1999;

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

  .  Notice of Annual Meeting and Proxy Statement for the 2000 Annual Meeting
     of Stockholders held on June 23, 2000;

  .  Current Reports on Form 8-K filed February 4, 2000 and October 20, 2000;
     and

  .  Our registration statement on Form S-4, No. 333-18725, as amended, which
     includes a description of our 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 200
  San Diego, CA 92121
  Attn: Chief Accounting Officer
  (858) 587-9333

                          FORWARD-LOOKING STATEMENTS

  This prospectus, including the documents that we incorporate by reference,
contains forward-looking statements within the meaning of Section 27A of the
Securities Act and Section 21E of the Exchange Act. Any statements about our
expectations, beliefs, plans, objectives, assumptions or future events or
performance are not historical facts and may be forward-looking. These
statements are often, but not always, made through the use of words or phrases
like "anticipate," "estimate," "plans," "projects," "continuing," "ongoing,"
"expects," "management believes," "the Company believes," "the Company
intends," "we believe," "we intend" and similar words or phrases. Accordingly,
these statements involve estimates, assumptions and uncertainties which could
cause actual results to differ materially from those expressed in them. Any
forward-looking statements are qualified in their entirety by reference to the
factors discussed throughout this prospectus. Among the key factors that could
cause actual results to differ materially from the forward-looking statements:

  .  risks and uncertainties regarding the adequacy of our clinical trial
     processes and whether the results of those clinical trials will be
     adequate to support regulatory filings and/or approvals;

  .  risks associated with timing of filing for regulatory approval of
     HE2000, and if regulatory approval is received, time to market
     thereafter;

                                       7
<PAGE>

  .  our ability to raise additional needed capital or consummate strategic
     or collaborative partner transactions on favorable terms or at all; and

  .  dependence on third party manufacturers of our products.

  Because the risk factors referred to above, as well as the risk factors
beginning on page 4 of this prospectus, could cause actual results or outcomes
to differ materially from those expressed in any forward-looking statements
made by us or on our behalf, you should not place undue reliance on any of
those forward-looking statements. Further, any forward-looking statement
speaks only as of the date on which it is made, and we undertake no obligation
to update any forward-looking statement to reflect events or circumstances
after the date on which the statement is made or to reflect the occurrence of
unanticipated events. New factors emerge from time to time, and it is not
possible for us to predict which factors will arise. In addition, we cannot
assess the impact of each factor on our business or the extent to which any
factor, or combination of factors, may cause actual results to differ
materially from those contained in any forward-looking statements.

                             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
5, 2000 which may be offered under the terms of this prospectus. This
information is based upon information provided by each selling stockholder.
Each selling shareholder is the beneficial owner of less than one percent of
our outstanding shares of Common Stock based on an aggregate of 11,589,525
shares issued and outstanding on November 28, 2000. The term "selling
stockholders" includes the stockholders listed below and their transferees,
pledges, donees or other successors. Each selling stockholder is offering all
of the shares they beneficially own, and assuming they sell every share, will
not beneficially own any shares of Hollis-Eden. 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.

<TABLE>
<CAPTION>
                                                                 Shares Being
                               Name                                Offered
                               ----                              ------------
   <S>                                                           <C>
   Jeffery L. Neuman, as TTEE pursuant to a Voting TR Agreement
    DTD 10/5/95 for beneficiaries Saltzman Partners, Cairnwood
    Inc. and Jeffery L. Neuman (1)..............................    61,231
   Jeffery L. Neuman as TTEE and sole beneficiary of Tudor
    Trust.......................................................     7,038
   Research Corporation Technologies, Inc. .....................    54,545
   Fort Washington Resources, Inc. .............................    41,173
   Temple University............................................    10,557
   Cairnwood, Inc. .............................................     7,038
   Saltzman Partners............................................     7,038
   Lawrence J. Schoenberg.......................................     5,278
   Pharmaceutics International, Inc. ...........................     4,926
   Janet Katz...................................................     3,870
   Carolinas HealthCare Systems.................................     2,111
   David P. Cohen...............................................     1,055
   Authur Schwartz and Karen Schwartz...........................     1,055
   Robert B. MacArthur..........................................       703
   Therapeutics, Inc............................................       703
   Edward W. McCloskey..........................................       351
   Tom and Jane Rogers..........................................    20,000
                                                                   -------
     Total......................................................   228,672
                                                                   =======
</TABLE>
--------
(1) Beneficial owners of shares listed consist of 20,355 by Saltzman Partners,
    20,438 shares by Cairnwood, Inc. and 20,438 by Jeffery L. Neuman.

                                       8
<PAGE>

                             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.

  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 under the terms of this prospectus. The selling stockholders may not sell
all of the shares. The selling stockholders may transfer, will 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 $4,257. 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).

                                       9
<PAGE>

                                 LEGAL MATTERS

  Cooley Godward LLP, San Diego, California will pass upon the validity of the
issuance of the common stock offered by this prospectus.

                                    EXPERTS

  The financial statements of the registrant as of December 31, 1999 and 1998,
and for each of the years ended December 31, 1999, 1998 and 1997, and for the
period August 15, 1994, the day we started doing business, to December 31,
1999, have been audited by BDO Seidman, LLP, as set forth in their report
included in Hollis-Eden's Annual Report on Form 10-K for the year ended
December 31, 1999. We incorporate these financial statements by reference into
this prospectus in reliance upon such report given upon the authority of BDO
Seidman, LLP as experts in accounting and auditing.

                                      10
<PAGE>

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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 5, 2000. You should not assume that this prospectus is accurate as of
any other date.
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                                228,672 Shares

                       HOLLIS-EDEN PHARMACEUTICALS, INC.

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

                                 Common Stock

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



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<PAGE>

                                    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............................................. $  257
       Legal fees and expenses..........................................  2,000
       Accounting fees and expenses.....................................  2,000
                                                                         ------
         Total.......................................................... $4,257
                                                                         ======
</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.

Item 16. Exhibits.

  (a) Exhibits.

<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-3.
</TABLE>

                                     II-1
<PAGE>

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>

                                  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 1,
2000.

                                          Hollis-Eden Pharmaceuticals, Inc.

                                                 /s/ Richard B. Hollis
                                          By: _________________________________
                                                     Richard B. Hollis
                                                 Chairman of the Board and
                                                  Chief Executive Officer

                               POWER OF ATTORNEY

  KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears
below constitutes and appoints Richard B. Hollis, Daniel D. Burgess 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 Board,        December 1, 2000
______________________________________  Chief Executive Officer
          Richard B. Hollis             and Director (Principal
                                        Executive Officer)

      /s/ Daniel D. Burgess            Chief Operating Officer/      December 1, 2000
______________________________________  Chief Financial Officer
          Daniel D. Burgess             (Principal Financial
                                        Officer)

       /s/ Robert W. Weber             Vice President-Controller/    December 1, 2000
______________________________________  Chief Accounting Officer
           Robert W. Weber              (Principal Accounting
                                        Officer)

      /s/ J. Paul Bagley III           Director                      December 1, 2000
______________________________________
          J. Paul Bagley III

       /s/ Leonard Makowka             Director                      December 1, 2000
______________________________________
           Leonard Makowka
</TABLE>

                                     II-3
<PAGE>

<TABLE>
<CAPTION>
              Signature                           Title                    Date
              ---------                           -----                    ----

<S>                                    <C>                          <C>
                                       Director                      December 1, 2000
______________________________________
         Brendan R. McDonnell

 /s/ Thomas Charles Merigan, Jr.       Chairman of the Scientific    December 1, 2000
______________________________________  Advisory Board and
     Thomas Charles Merigan, Jr.        Director

                                       Director                      December 1, 2000
______________________________________
          William H. Tilley

      /s/ Salvatore J. Zizza           Director                      December 1, 2000
______________________________________
          Salvatore J. Zizza
</TABLE>

                                      II-4
<PAGE>

                                 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-3.
</TABLE>


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